Well I can guess that the games worked in full screen before on the same equipment (by that I mean the same monitor) which would put one of my theories to one side (monitor doesn’t support 640x480 resolution) and even changing between XP MCE and XP Pro wouldn’t produce these problems so I’m guessing that there’s a refresh rate issue which can be fixed by forcing every game to run at a pre determined refresh rate.
the link and information in the second post of the thread I’ve linked to should help even though the information is for another game it is relevant for your problem.