Despite what resolution I set with realMYSTSetup.exe I keep playing in 800 x 600. So I decided to take matters into my own hands and peek into some files. I found that the resolution can be set in the file WIN_INIT.DAT I also found a line or two that were interesting.
ScreenSize ColorDepth FullScreen
ScreenSize and ColorDepth are easy enoy enough to figure out but FullScreen is giving me a hassle of a time figuring out. I don't think it's boolean and I think it can be replaced with Window but again I am having trouble tweaking it to make a windowed mode happen. If anyone can lend a hand I wouldn't be the only one to appreciate it. I'm sure there is a windowed mode we just haven't seen the documentation for it yet.