Actually a lot of old games have such behavior of changing Xserver resolution. This should be your cure:I need the window mode (and therefore 32 bit colors) or it changes my desktop resolution to 640x480 (even after I close the game).
I tried switching hardware acceleration on and off, but it seems to change nothing, probably my graphics card isn't involved anyways.
I installed d3dx9, I'll tell you later if this changes anything.
http://askubuntu.com/questions/123159/h ... lay-layout
Alternatively, you can run "xrandr -s 0" in a terminal after closing the game to go back to the normal resolution.