If your getting warnings with 3.6.12 and Zathras please post what they are. Since you already ran a debug build post the fs2_open.log from that as well.
Okay, after using a 3.6.9INF pilot with 3.6.12dINF and Zathras 2.0, I didn't get any warnings with the Vorlon campaign any more, but when testing MAG's Twilight Struggle I get:
Unknown flag2 in mission file: no-bank
<no module>! KiFastSystemCallRet
<no module>! WaitForSingleObject + 18 bytes
<no module>! SCP_DumpStack + 354 bytes
<no module>! Warning + 430 bytes
<no module>! parse_object + 3105 bytes
<no module>! parse_objects + 192 bytes
<no module>! parse_mission + 505 bytes
<no module>! parse_main + 449 bytes
<no module>! mission_load + 215 bytes
<no module>! game_start_mission + 198 bytes
<no module>! game_enter_state + 482 bytes
<no module>! gameseq_set_state + 310 bytes
<no module>! game_process_event + 242 bytes
<no module>! gameseq_process_events + 152 bytes
<no module>! game_main + 782 bytes
<no module>! WinMain + 330 bytes
<no module>! __tmainCRTStartup + 358 bytes
<no module>! WinMainCRTStartup + 15 bytes
<no module>! RegisterWaitForInputIdle + 73 bytes
When starting the launcher a second time I get directly on startup:
Starfield bitmap 'xparent' already listed as a xparentxparent bitmap!! Only using the xparent version!
<no module>! KiFastSystemCallRet
<no module>! WaitForSingleObject + 18 bytes
<no module>! SCP_DumpStack + 354 bytes
<no module>! Warning + 430 bytes
<no module>! parse_startbl + 476 bytes
<no module>! parse_modular_table + 267 bytes
<no module>! stars_init + 82 bytes
<no module>! game_init + 1998 bytes
<no module>! game_main + 519 bytes
<no module>! WinMain + 330 bytes
<no module>! __tmainCRTStartup + 358 bytes
<no module>! WinMainCRTStartup + 15 bytes
<no module>! RegisterWaitForInputIdle + 73 bytes
After turning Zathras off I get:
An ai profile named 'FS2 RETAIL' already exists! The new one will not be created.
<no module>! KiFastSystemCallRet
<no module>! WaitForSingleObject + 18 bytes
<no module>! SCP_DumpStack + 354 bytes
<no module>! Warning + 430 bytes
<no module>! parse_ai_profiles_tbl + 510 bytes
<no module>! ai_profiles_init + 110 bytes
<no module>! game_init + 1910 bytes
<no module>! game_main + 519 bytes
<no module>! WinMain + 330 bytes
<no module>! __tmainCRTStartup + 358 bytes
<no module>! WinMainCRTStartup + 15 bytes
<no module>! RegisterWaitForInputIdle + 73 bytes
I get similar warnings with several of MAG's Star Fury pilot missions while all of them are fine with 3.6.9. Looking at the logs I think most of them are connected to the missions themselves and I could fix them with my patch, but why is 3.6.12 so incompatible? Even after cloning a pilot in 3.6.12d_INF the Battle of the line crashes with:
Malloc Failed!
<no module>! KiFastSystemCallRet
<no module>! CreateThread + 30 bytes
<no module>! SCP_DumpStack + 278 bytes
<no module>! Error + 229 bytes
<no module>! _vm_malloc + 121 bytes
<no module>! ds_load_buffer + 774 bytes
<no module>! snd_load + 1016 bytes
<no module>! message_load_wave + 199 bytes
<no module>! message_pagein_mission_messages + 175 bytes
<no module>! level_page_in + 171 bytes
<no module>! freespace_mission_load_stuff + 206 bytes
<no module>! game_post_level_init + 182 bytes
<no module>! game_start_mission + 387 bytes
<no module>! game_enter_state + 482 bytes
<no module>! gameseq_set_state + 310 bytes
<no module>! game_process_event + 242 bytes
<no module>! gameseq_process_events + 152 bytes
<no module>! game_main + 782 bytes
<no module>! WinMain + 330 bytes
<no module>! __tmainCRTStartup + 358 bytes
<no module>! WinMainCRTStartup + 15 bytes
<no module>! RegisterWaitForInputIdle + 73 bytes
Also I noticed that in the Vorlon campaign the first level is stuttering much more than with the 3.6.9 inferno build and that in Twilight Struggle whenever a Narn cruiser explodes black squares are visible around the explosions.