The missile issue sounds a lot like a corrupt pilot file. You should have had them in the training missions with the 107th Ravens, and during the missions from there on. The solution is to create a new pilot. I know, it's not a pleasant solution but it should work.
Playing more Freespace 2 never hurts =D I'm only on like the tenth mission anyways.
And I was wondering about that previous picture. I thought you were mad at us for some reason.
Of course not! I am very grateful for your help! And that picture was a facebook graffiti I drew for a friend of mine that couldn't be saved due to a bug.
Black rectangles issue is (or at least used to be) an old issue related to additional game data files (certain graphic files in old mediavps had black alpha instead of having no alpha). You must be using older set of vp files than even the 3.6.8 zeta mediavps. Get the newer set of files.
I see. Where might I find these newer medivps files? None of the files here
http://www.fsoinstaller.com/files/installer/ seem to be it.
Yep. I suspect the 710 patches are missing. Joe22c, before you go any further you should run the fs2_open_3_6_9_debug.exe. This will create a new file in your data folder called fs2_open.log Once you post that we'll be in a much better position to tell what you are missing and what you have that you shouldn't have. You don't need to actually play the game, simply get to the mainhall and quit.
K, Im going to go download this debug.exe thing right now.
UPDATE:
ok, well I couldn't find the EXACT debug.exe you spoke of, so I got this instead

I'm thinking it'll be just as good.
Upon running it, here be my log:
==========================================================================
DEBUG SPEW: No debug_filter.cfg found, so only general, error, and warning
categories can be shown and no debug_filter.cfg info will be saved.
==========================================================================
FreeSpace version: 3.6.10
Passed cmdline options:
-mipmap
-missile_lighting
-glow
-spec
-ballistic_gauge
-dualscanlines
-rearm_timer
-targetinfo
-3dwarp
-warp_flash
-snd_preload
-mod mediavps
Building file index...
Found root pack 'D:\games\freespace 2\freespace 2\freespace2\mediavps\mv_core.vp' with a checksum of 0x730213f0
Found root pack 'D:\games\freespace 2\freespace 2\freespace2\mediavps\mv_effects.vp' with a checksum of 0xc884a83f
Found root pack 'D:\games\freespace 2\freespace 2\freespace2\mediavps\mv_models.vp' with a checksum of 0x99dc16c5
Found root pack 'D:\games\freespace 2\freespace 2\freespace2\mediavps\mv_music.vp' with a checksum of 0x89430ae4
Found root pack 'D:\games\freespace 2\freespace 2\freespace2\mediavps\mv_textures.vp' with a checksum of 0x94b763d1
Found root pack 'D:\games\freespace 2\freespace 2\freespace2\mediavps\data\HTL_Moloch.vp' with a checksum of 0x874ec910
Found root pack 'D:\games\freespace 2\freespace 2\freespace2\mediavps\data\NaRR10_Nebulae.vp' with a checksum of 0x5985ba1d
Found root pack 'D:\games\freespace 2\freespace 2\freespace2\root_fs2.vp' with a checksum of 0xce10d76c
Found root pack 'D:\games\freespace 2\freespace 2\freespace2\smarty_fs2.vp' with a checksum of 0xddeb3b1e
Found root pack 'D:\games\freespace 2\freespace 2\freespace2\sparky_fs2.vp' with a checksum of 0x164fe65a
Found root pack 'D:\games\freespace 2\freespace 2\freespace2\sparky_hi_fs2.vp' with a checksum of 0xa11d56f1
Found root pack 'D:\games\freespace 2\freespace 2\freespace2\stu_fs2.vp' with a checksum of 0xd77da83a
Found root pack 'D:\games\freespace 2\freespace 2\freespace2\tango1_fs2.vp' with a checksum of 0x4c25221e
Found root pack 'D:\games\freespace 2\freespace 2\freespace2\tango2_fs2.vp' with a checksum of 0x86920b82
Found root pack 'D:\games\freespace 2\freespace 2\freespace2\tango3_fs2.vp' with a checksum of 0x705e8d71
Found root pack 'D:\games\freespace 2\freespace 2\freespace2\warble_fs2.vp' with a checksum of 0xd85c305d
Searching root 'D:\games\freespace 2\freespace 2\freespace2\mediavps\' ... 92 files
Searching root pack 'D:\games\freespace 2\freespace 2\freespace2\mediavps\mv_core.vp' ... 85 files
Searching root pack 'D:\games\freespace 2\freespace 2\freespace2\mediavps\mv_effects.vp' ... 739 files
Searching root pack 'D:\games\freespace 2\freespace 2\freespace2\mediavps\mv_models.vp' ... 311 files
Searching root pack 'D:\games\freespace 2\freespace 2\freespace2\mediavps\mv_music.vp' ... 15 files
Searching root pack 'D:\games\freespace 2\freespace 2\freespace2\mediavps\mv_textures.vp' ... 1527 files
Searching root pack 'D:\games\freespace 2\freespace 2\freespace2\mediavps\data\HTL_Moloch.vp' ... 1 files
Searching root pack 'D:\games\freespace 2\freespace 2\freespace2\mediavps\data\NaRR10_Nebulae.vp' ... 225 files
Searching root 'D:\games\freespace 2\freespace 2\freespace2\' ... 7 files
Searching root pack 'D:\games\freespace 2\freespace 2\freespace2\root_fs2.vp' ... 157 files
Searching root pack 'D:\games\freespace 2\freespace 2\freespace2\smarty_fs2.vp' ... 10 files
Searching root pack 'D:\games\freespace 2\freespace 2\freespace2\sparky_fs2.vp' ... 3027 files
Searching root pack 'D:\games\freespace 2\freespace 2\freespace2\sparky_hi_fs2.vp' ... 1337 files
Searching root pack 'D:\games\freespace 2\freespace 2\freespace2\stu_fs2.vp' ... 2355 files
Searching root pack 'D:\games\freespace 2\freespace 2\freespace2\tango1_fs2.vp' ... 32 files
Searching root pack 'D:\games\freespace 2\freespace 2\freespace2\tango2_fs2.vp' ... 15 files
Searching root pack 'D:\games\freespace 2\freespace 2\freespace2\tango3_fs2.vp' ... 10 files
Searching root pack 'D:\games\freespace 2\freespace 2\freespace2\warble_fs2.vp' ... 52 files
Searching root 'g:\' ... 0 files
Found 19 roots and 9997 files.
Setting language to English
Initializing OpenAL...
Using 'Generic Software' as OpenAL sound device...
OpenAL Vendor : Creative Labs Inc.
OpenAL Renderer : Software
OpenAL Version : 1.1
... OpenAL successfully initialized!
Failed to init speech
GR_CPU: Family 6, MMX=Yes
Initializing OpenGL graphics device at 1024x768 with 16-bit color...
Initializing WGL...
Requested WGL Video values = R: 5, G: 6, B: 5, depth: 16, double-buffer: 1
Actual WGL Video values = R: 8, G: 8, B: 8, depth: 32, double-buffer: 1
OpenGL Vendor : ATI Technologies Inc.
OpenGL Renderer : RADEON 8500 DDR x86/MMX/3DNow!/SSE
OpenGL Version : 1.3.1062 WinXP Release
Using extension "GL_EXT_fog_coord".
Using extension "GL_ARB_multitexture".
Using extension "GL_ARB_texture_env_add".
Using extension "GL_ARB_texture_compression".
Using extension "GL_EXT_texture_compression_s3tc".
Using extension "GL_EXT_texture_filter_anisotropic".
Using extension "GL_ARB_texture_env_combine".
Using extension "GL_EXT_compiled_vertex_array".
Using extension "GL_EXT_draw_range_elements".
Using extension "GL_ARB_texture_mirrored_repeat".
Unable to find extension "GL_ARB_texture_non_power_of_two".
Using extension "GL_ARB_vertex_buffer_object".
Unable to find extension "GL_EXT_pixel_buffer_object".
Using extension "GL_SGIS_generate_mipmap".
Unable to find extension "GL_EXT_framebuffer_object".
Using extension "GL_EXT_texture_rectangle".
Using extension "GL_EXT_bgra".
Using extension "GL_ARB_texture_cube_map".
Using extension "GL_EXT_texture_lod_bias".
Unable to find extension "NV_point_sprite".
Unable to find extension "GL_ARB_shading_language_100".
Unable to find extension "GL_ARB_shader_objects".
Unable to find extension "GL_ARB_vertex_shader".
Unable to find extension "GL_ARB_fragment_shader".
Found special extension function "wglSwapIntervalEXT".
Max texture units: 6 (6)
Max elements vertices: 2147483647
Max elements indices: 65535
Max texture size: 2048x2048
Can use compressed textures: YES
Texture compression available: YES
Using trilinear texture filter.
... OpenGL init is complete!
Size of bitmap info = 705 KB
Size of bitmap extra info = 40 bytes
ANI cursorweb with size 24x24 (25.0% wasted)
GRAPHICS: Initializing default colors...
SCRIPTING: Beginning initialization sequence...
SCRIPTING: Beginning Lua initialization...
LUA: Opening LUA state...
LUA: Initializing base Lua libraries...
LUA: Performing global function/(library/object) name repeat check...
LUA: Performing library/object name repeat check...
LUA: Performing object/object name repeat check...
LUA: Performing library/library name repeat check...
LUA: Initializing library functions...
LUA: Initializing object functions...
SCRIPTING: Beginning main hook parse sequence....
Wokka! Error opening file (scripting.tbl)!
TABLES: Unable to parse 'scripting.tbl'! Error code = 5.
SCRIPTING: Inititialization complete.
Using high memory settings...
Wokka! Error opening file (interface.tbl)!
WMCGUI: Unable to parse 'interface.tbl'! Error code = 5.
ANI 2_radar1 with size 170x170 (33.6% wasted)
Windoze reported 16 joysticks, we found 0
Current soundtrack set to -1 in event_music_reset_choices
TBM => Starting parse of 'mv_music-mus.tbm' ...
Wokka! Error opening file (armor.tbl)!
TABLES: Unable to parse 'armor.tbl'! Error code = 5.
TBM => Starting parse of 'mv_effects-wxp.tbm' ...
BMPMAN: Found EFF (exp20.eff) with 64 frames at 35 fps.
ANI Lamprey_Impact with size 80x80 (37.5% wasted)
TBM => Starting parse of 'mv_models-wep.tbm' ...
TBM => Starting parse of 'mv_flak-wep.tbm' ...
TBM => Starting parse of 'mv_effects-wep.tbm' ...
TBM => Starting parse of 'mv_shockwave-wep.tbm' ...
TBM => Starting parse of 'mv_tech-wep.tbm' ...
TBM => Starting parse of 'mv_textures-shp.tbm' ...
TBM => Starting parse of 'mv_models-shp.tbm' ...
TBM => Starting parse of 'mv_trails-shp.tbm' ...
TBM => Starting parse of 'mv_shockwave-shp.tbm' ...
TBM => Starting parse of 'mv_turretangle-shp.tbm' ...
WARNING: Animation trigger #0 on subsystem 'turret01a', for ship 'GTB Medusa', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret01', for ship 'GTFR Triton', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret02', for ship 'GTFR Triton', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret09a-01-main', for ship 'GTC Fenris', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret01', for ship 'GTM Hippocrates', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret02', for ship 'GTM Hippocrates', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret03', for ship 'GTM Hippocrates', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret09a-01-main', for ship 'GTC Leviathan', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret01a', for ship 'GTD Orion', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret02a', for ship 'GTD Orion', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret03a', for ship 'GTD Orion', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret04a', for ship 'GTD Orion', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret05a', for ship 'GTD Orion', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret01', for ship 'GTD Hecate', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret02', for ship 'GTD Hecate', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret03', for ship 'GTD Hecate', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret04', for ship 'GTD Hecate', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret05', for ship 'GTD Hecate', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret06', for ship 'GTD Hecate', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret07', for ship 'GTD Hecate', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret08', for ship 'GTD Hecate', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret01a', for ship 'GTD Orion#2 (Bastion)', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret02a', for ship 'GTD Orion#2 (Bastion)', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret03a', for ship 'GTD Orion#2 (Bastion)', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret04a', for ship 'GTD Orion#2 (Bastion)', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret05a', for ship 'GTD Orion#2 (Bastion)', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret01a', for ship 'GTVA Colossus', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret02a', for ship 'GTVA Colossus', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret03a', for ship 'GTVA Colossus', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret04a', for ship 'GTVA Colossus', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret05a', for ship 'GTVA Colossus', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret06a', for ship 'GTVA Colossus', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret07a', for ship 'GTVA Colossus', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret08a', for ship 'GTVA Colossus', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret09a', for ship 'GTVA Colossus', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret10a', for ship 'GTVA Colossus', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret01', for ship 'GTCv Deimos', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret02', for ship 'GTCv Deimos', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret03', for ship 'GTCv Deimos', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret04', for ship 'GTCv Deimos', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret01', for ship 'GTC Aeolus', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret02', for ship 'GTC Aeolus', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret03', for ship 'GTC Aeolus', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret04', for ship 'GTC Aeolus', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret05', for ship 'GTC Aeolus', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret06', for ship 'GTC Aeolus', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret01a', for ship 'NTF Iceni', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret11a', for ship 'NTF Iceni', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret19', for ship 'NTF Iceni', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret21a', for ship 'NTF Iceni', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret22a', for ship 'NTF Iceni', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret23a', for ship 'NTF Iceni', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret24a', for ship 'NTF Iceni', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret25a', for ship 'NTF Iceni', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret01', for ship 'GTT Argo', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret02', for ship 'GTT Argo', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'Turret01-main', for ship 'GVFr Satis', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret01a', for ship 'GVC Aten', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret02a', for ship 'GVC Aten', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret01', for ship 'GVC Mentu', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret02', for ship 'GVC Mentu', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret15', for ship 'GVC Mentu', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret16', for ship 'GVC Mentu', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret01', for ship 'GVCv Sobek', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret02', for ship 'GVCv Sobek', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret03', for ship 'GVCv Sobek', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret05', for ship 'GVCv Sobek', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret07', for ship 'SC Cain', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret07', for ship 'SC Lilith', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret01', for ship 'SFr Mephisto', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret03', for ship 'SFr Mephisto', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret03a-base', for ship 'SD Demon', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret06a-base', for ship 'SD Demon', has a negative reverse_start value! Capping it at 0!
WARNING: Animation trigger #0 on subsystem 'turret07a-base', for ship 'SD Demon', has a negative reverse_start value! Capping it at 0!
TBM => Starting parse of 'mv_tech-shp.tbm' ...
loading animated cursor "cursor"
ANI cursor with size 24x24 (25.0% wasted)
Ships.tbl is : VALID
Weapons.tbl is : VALID
cfile_init() took 1740
MOVIE ERROR: Unable to open movie file 'intro.mve' in any supported format.
Got event GS_EVENT_GAME_INIT (49) in state NOT A VALID STATE (0)
ANI cursor.ani with size 24x24 (25.0% wasted)
Frame 0 too long!!: frametime = 0.497 (0.497)
Frame 0 too long!!: frametime = 0.849 (0.849)
Got event GS_EVENT_MAIN_MENU (0) in state GS_STATE_INITIAL_PLAYER_SELECT (37)
Someone passed an extension to bm_load for file '242suicide.pcx'
ANI 2_mainwalk.ani with size 477x477 (6.8% wasted)
ANI 2_mainflyby.ani with size 189x189 (26.2% wasted)
ANI 2_maincrane.ani with size 116x116 (9.4% wasted)
ANI 2_mainexit.ani with size 174x174 (32.0% wasted)
ANI 2_mainbarracks.ani with size 158x158 (38.3% wasted)
ANI 2_mainreadyroom.ani with size 145x145 (43.4% wasted)
ANI 2_maintechroom.ani with size 119x119 (7.0% wasted)
ANI 2_mainoptions.ani with size 206x206 (19.5% wasted)
ANI 2_maincampaign.ani with size 190x190 (25.8% wasted)
Frame 0 too long!!: frametime = 2.315 (2.315)
Frame 0 too long!!: frametime = 0.659 (0.659)
Got event GS_EVENT_QUIT_GAME (5) in state GS_STATE_MAIN_MENU (1)
Freeing all existing models...
... Log closed, Wed Mar 12 23:38:28 2008