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I have multiple monitors (three to be exact) and whenever I try to run the program it always shows up in the left monitor instead of the center (main) monitor. Then whenever I try to click on anything in the game (like the new game button) the program goes out of focus as if I had clicked somewhere outside the game screen. I can't really seem to find a solution to this myself but does anyone know a solution?
This question / problem has been solved by Marvinimage
http://www.gog.com/forum/system_shock_2/if_youre_using_custom_user_mode_resolutions_and_cant_see_them_ingame
Except I can't do that! When I try to click on the options button in the menu it leaves the program like I mentioned, or is he talking about choosing a hardware device somewhere in the actual game files?
It could also be a driver or windows problem. Have you tried different monitor settings in Catalyst/Nvidia software center, like disabling certain monitors, extending them, etc.?
try running windowed (see the sticky/useful links), that should allow you to modify the video options. by default, the game should pick the primary monitor.