I think I answered this by email earlier today

Basically I expect your monitor is setup for horizontal games (usually ~240-256 lines), in which case some of the top/bottom lines will be cut of of your 288 line setup.
Try using 360x240, IMO this is a much nicer res as it doesn't appear stretched like 640x288

Edit: Just thought I'd add that 640x480 is interlaced which is why it flickers, so generally avoid that res if possible...