Never mind, I got it working, but now I cant load my save games! 
Mind explaining how you got it working and what exactly was the issue in your case?
I have some similar issues - parts of menu can turn pink and the game will crash if said menu is revisited.
Also, for some obscure reason, the skybox textures in SHTUP crash my game always when loading a save or starting a new game. Some other users also have reported this weird problem in the SHTUP thread.
However, Rebirth complemented, Tacticool weapons and Hi-res player model mods work flawlessly. I haven't tried any other mods with this SS2 installation.
Backgound info:
Windows 2003 x64, ATI HD3800 series GFX card, Catalyst 9.5 drivers.
I have clean copy of System Shock 2 version 1.15 that I've installed by copying the \SHOCK\ directory from the CD to G:\GAMES\SS2\, then ran SS2Tool with all options checked.
I've played around with many of the settings and have found that the memory allocation in LG.INI appears to somehow affect the frequency of those seemingly random "pink menu crashes".
ddfix is applied correctly and in use.
Video fix is disabled and I've deleted LGVID.AX. (I don't care about the videos)
ddfix compatibility settings are default (UseSysMemOverlay=2, OverlayColourKey=0xf81f). Tried 0 to both, but that changed nothing.
I wish I knew what these compatibility settings actually do. Are they documented anywhere?
http://timeslip.chorrol.com/ddfix.html seems to be down.