This is the debug log I get when I make FSO use a font made with the original fonttool and edited in fonttool2:
==========================================================================
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: 3.6.11.1111
Passed cmdline options:
  -spec_exp 7.0
  -fov 0.65
  -spec_static 3.0
  -spec_point 8.6
  -spec_tube 5.0
  -ambient_factor 130
  -mipmap 
  -missile_lighting 
  -glow 
  -spec 
  -normal 
  -3dshockwave 
  -post_process 
  -cache_bitmaps 
  -ballistic_gauge 
  -dualscanlines 
  -rearm_timer 
  -targetinfo 
  -3dwarp 
  -ship_choice_3d 
  -weapon_choice_3d 
  -warp_flash 
  -snd_preload 
  -mod pprocess,Landreich
  -wcsaga 
Building file index...
Found root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_anims.vp' with a checksum of 0x20ede0b2
Found root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_core.vp' with a checksum of 0x2c725bc9
Found root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_effects.vp' with a checksum of 0xb0272d7b
Found root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_hud.vp' with a checksum of 0x0a624b02
Found root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_interface.vp' with a checksum of 0x17c4567c
Found root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_music.vp' with a checksum of 0x244979b7
Found root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_ships.vp' with a checksum of 0x4248ea63
Found root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_sounds.vp' with a checksum of 0xda87e6ba
Found root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_voice.vp' with a checksum of 0x3066cebf
Found root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\wc3_demo.vp' with a checksum of 0xd5a282a0
Found root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\wc4_campaign_0.23.vp' with a checksum of 0x16c4e490
Found root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\wc4_core_0.23.vp' with a checksum of 0x331bb657
Searching root 'C:\Program Files\Games\Wing Commander Saga Prologue\pprocess\' ... 40 files
Searching root 'C:\Program Files\Games\Wing Commander Saga Prologue\Landreich\' ... 1020 files
Searching root 'C:\Program Files\Games\Wing Commander Saga Prologue\' ... 84 files
Searching root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_anims.vp' ... 3 files
Searching root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_core.vp' ... 60 files
Searching root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_effects.vp' ... 245 files
Searching root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_hud.vp' ... 205 files
Searching root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_interface.vp' ... 1313 files
Searching root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_music.vp' ... 37 files
Searching root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_ships.vp' ... 1167 files
Searching root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_sounds.vp' ... 157 files
Searching root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\prologue_voice.vp' ... 685 files
Searching root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\wc3_demo.vp' ... 62 files
Searching root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\wc4_campaign_0.23.vp' ... 183 files
Searching root pack 'C:\Program Files\Games\Wing Commander Saga Prologue\wc4_core_0.23.vp' ... 340 files
Found 15 roots and 5601 files.
Setting language to English
TBM  =>  Starting parse of 'difficulty-lcl.tbm' ...
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
Initializing OpenGL graphics device at 1280x1024 with 32-bit color...
  Initializing WGL...
  Requested WGL Video values = R: 8, G: 8, B: 8, depth: 32, double-buffer: 1
  Actual WGL Video values    = R: 8, G: 8, B: 8, depth: 32, double-buffer: 1
  OpenGL Vendor     : NVIDIA Corporation
  OpenGL Renderer   : GeForce 9800 GT/PCI/SSE2
  OpenGL Version    : 3.1.0
  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".
  Using extension "GL_ARB_texture_non_power_of_two".
  Using extension "GL_ARB_vertex_buffer_object".
  Using extension "GL_ARB_pixel_buffer_object".
  Using extension "GL_SGIS_generate_mipmap".
  Using extension "GL_EXT_framebuffer_object".
  Using extension "GL_ARB_texture_rectangle".
  Using extension "GL_EXT_bgra".
  Using extension "GL_ARB_texture_cube_map".
  Using extension "GL_EXT_texture_lod_bias".
  Using extension "GL_ARB_point_sprite".
  Using extension "GL_ARB_shading_language_100".
  Using extension "GL_ARB_shader_objects".
  Using extension "GL_ARB_vertex_shader".
  Using extension "GL_ARB_fragment_shader".
  Using extension "GL_NV_vertex_program3".
  Found special extension function "wglSwapIntervalEXT".
Initializing Shaders Manager...
Loading and compiling main shaders...
  Compiling main shader ->  main-v.sdr (null-v.sdr) / main-f.sdr (null-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (b-v.sdr) / main-f.sdr (b-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (b-v.sdr) / main-f.sdr (bg-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (l-v.sdr) / main-f.sdr (lb-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (l-v.sdr) / main-f.sdr (lbg-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (l-v.sdr) / main-f.sdr (lbgs-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (l-v.sdr) / main-f.sdr (lbs-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (ln-v.sdr) / main-f.sdr (lbgn-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (ln-v.sdr) / main-f.sdr (lbgsn-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (ln-v.sdr) / main-f.sdr (lbn-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (ln-v.sdr) / main-f.sdr (lbsn-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (lf-v.sdr) / main-f.sdr (lfb-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (lf-v.sdr) / main-f.sdr (lfbg-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (lf-v.sdr) / main-f.sdr (lfbgs-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (lf-v.sdr) / main-f.sdr (lfbs-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (lfn-v.sdr) / main-f.sdr (lfbgn-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (lfn-v.sdr) / main-f.sdr (lfbgsn-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (lfn-v.sdr) / main-f.sdr (lfbn-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (lfn-v.sdr) / main-f.sdr (lfbsn-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (l-v.sdr) / main-f.sdr (null-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (l-v.sdr) / main-f.sdr (lg-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (l-v.sdr) / main-f.sdr (lgs-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (l-v.sdr) / main-f.sdr (ls-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (ln-v.sdr) / main-f.sdr (lgn-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (ln-v.sdr) / main-f.sdr (lgsn-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (ln-v.sdr) / main-f.sdr (ln-f.sdr) ... 
  Compiling main shader ->  main-v.sdr (ln-v.sdr) / main-f.sdr (lsn-f.sdr) ... 
Shaders Manager initialized.
  Max texture units: 4 (32)
  Max elements vertices: 1048576
  Max elements indices: 1048576
  Max texture size: 8192x8192
  Can use compressed textures: YES
  Texture compression available: YES
  Using trilinear texture filter.
  Using GLSL for model rendering.
  Shader Version: 1.40 NVIDIA via Cg compiler
... OpenGL init is complete!
Size of bitmap info = 760 KB
Size of bitmap extra info = 52 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: Beginning ADE initialization
ADE: Initializing enumeration constants...
ADE: Assigning Lua session...
SCRIPTING: Beginning main hook parse sequence....
Wokka!  Error opening file (scripting.tbl)!
TABLES: Unable to parse 'scripting.tbl'!  Error code = 5.
SCRIPTING: Inititialization complete.
I get a Microsoft Visual C++ Debug Error (invalid allocation size) if I try to use a font made with fonttool2 on a debug build and a "Malloc failed!" on a release build.  The debug log is the same.
Again, did anyone have any luck compiling fonttool from the icculus repo or the original source code release?