have you tried patch 1 which was posted on this forum thread or patch 2 from the sticky one?
w_w_w_.gog.com/forum/system_shock_series/currently_known_problems_and_solutions/page1
iareth: Hi guys, I had the same "SS has stopped working" problem in 64-bit Windows 7 and nothing seemed to help. I tried installing the new executable, removing Raptr and fiddling around with the ini file to no avail. I got an instant crash as soon as the Origin logo appeared.
Then I realized that my selected MIDI mapper was MT32 emulator. So I changed that to CoolSynth with GM soundfont, and presto! Now the enhanced edition seems to run smoothly and without crashes.
Because quite a few other retro gamers may also use MT32 emulation (or even have a real one plugged in), if you run into problems, be sure to check which midi mapper you have selected. It would be nice if future builds would check the active midi device on launch and let the user know whether s/he is using an unsupported device.