OK, I've gotten a re-producible crash in the first reactor. Happens when the game attempts to enter a battle against enemy SPAA on the pipe above the save point. I've installed Nightmare using the .040RC version of Bootleg, so this may in actual fact be a Bootleg issue.
INFO: FF7/FF8 OpenGL driver version 0.7.11b
INFO: Auto-detected version: FF7 1.02 US English
INFO: NVIDIA Corporation GeForce GTX 570/PCIe/SSE2 4.2.0
INFO: OpenGL 2.0 support detected
INFO: Using PBO
INFO: Found swap_control extension
INFO: Max texture size: 16384x16384
INFO: Number of texture units: 4
INFO: Original resolution 640x480, window size 1920x1080, output resolution 1440x1080, internal resolution 3840x2160
INFO: FBO extension detected, using fast scaling/postprocessing path
INFO: Shader limits: varying 124, vert uniform 4096, frag uniform 2048
INFO: fragment shader compile log:
0(20) : warning C7508: extension ARB_framebuffer_object not supported
INFO: postprocessing program link log:
Fragment info
-------------
0(20) : warning C7508: extension ARB_framebuffer_object not supported
0(264) : warning C7050: "ao" might be used before being initialized
INFO: FFMpeg movie player plugin loaded
INFO: FFMpeg version SVN-r25886, Copyright (c) 2000-2010 Fabrice Bellard, et al.
INFO: FF7Music helper plugin loaded
INFO: Loading external library Multi.dll
LOCK UNLOCK TEST
MATRIX INITIALIZE
INITIALIZE DD/D3D END
initializing sound...
creating dsound primary buffer
reading audio file
loading static sounds
sound initialized
set music volume: 127
set music volume: 127
Entering MAIN
Exiting MAIN
START OF CREDITS!!!
ERROR: couldn't open movie file: Z:\Games\FF7\movies\eidoslogo.avi
INFO: Z:\Games\FF7\movies\sqlogo.avi; h264/aac 1280x896, 15.000000 FPS, duration: 14.533333, frames: 218
set music volume trans: 127->0, step=60
END OF CREDITS!!!
Entering MAIN
set music volume: 127
Exiting MAIN
START OF MENU SYSTEM!!!
END OF MENU SYSTEM!!!
Entering MAIN
Exiting MAIN
Field Start
Entering MAIN
Exiting MAIN
START OF MENU SYSTEM!!!
END OF MENU SYSTEM!!!
Entering MAIN
Exiting MAIN
Field Start
Field Quit
Entering MAIN
Exiting MAIN
Entering FRAME_INITIALIZE SWIRL
Exitting FRAME_INITIALIZE SWIRL
Swirl sound_effect1
stop_sound
End of Swirl sound_effect1
Entering FRAME_QUIT SWIRL
Exitting FRAME_QUIT SWIRL
Entering MAIN
Exiting MAIN
[BATTLE] Entering FRAME_INITIALIZE
[BATTLE] Scene# 318
[BATTLE] Exitting FRAME_INITIALIZE
[BATTLE] Begin main battle loop
[BATTLE] End of current battle
[BATTLE] Begin end battle stuff
stop_sound
[BATTLE] Entering FRAME_QUIT
[BATTLE] endof battle.
[BATTLE] Exitting FRAME_QUIT
Entering MAIN
Exiting MAIN
START OF MENU SYSTEM!!!
END OF MENU SYSTEM!!!
Entering MAIN
Exiting MAIN
Field Start
cross play music: 0
set music volume trans: 127->0, step=4
set music volume: 127
Field Quit
Entering MAIN
Exiting MAIN
Entering FRAME_INITIALIZE SWIRL
Exitting FRAME_INITIALIZE SWIRL
Swirl sound_effect1
stop_sound
End of Swirl sound_effect1
Entering FRAME_QUIT SWIRL
Exitting FRAME_QUIT SWIRL
Entering MAIN
Exiting MAIN
[BATTLE] Entering FRAME_INITIALIZE
[BATTLE] Scene# 321
[BATTLE] Exitting FRAME_INITIALIZE
ERROR: failed to find file battle/SPAA (LGP) (path: FF7/DATA/BATTLE/EFFECT/HITMARK)
ERROR: offset error: ENEMY483.D SPAA
ERROR: could not open file ENEMY483.D
ERROR: unhandled exception
Thoughts?