I've this problem too in my game... I use Windows ME and I've a 32 bit colour game:
My starting Windows resolution is 1024x768 and I've a 17'' monitor flat in front but CRT (is it right ? CRT means that the monitor have a back long)
640x480 black area upper and right
320x240 ehy, this didn't work now... boh.
This is a problem I didn't consider too much. But Remember to test the return code of the Install functions, to prevent and notify errors during the setup of your games..