[color:"orange"]I didn't have the intro skipped, because it only happens during game play.[/color]
Skipping the intro videos will allow you to play most of the time without the play CD in an optical drive. This in turn should prevent whatever is periodically checking the drive from causing it to spin up and minimize the game.
[color:"orange"]Does the monitor refresh rate have anything to do with the flickering?[/color]
What flickering? During gameplay, or when DirectX is switching resolutions?
If you do not notice any flickering in Windows, then the monitor refresh rate probably isn't an issue with the game. The refresh rate might drop switching to a higher resolution than your desktop, but shouldn't at a lower resolution.
[color:"orange"]my system resolution is 1024x768, but DD config is 640x480, does that matter?[/color]
It shouldn't. In general, whether a problem gets worse, better or stays the same when changing resolutions could help narrow down the source of the problem.
A couple people playing Beyond Divinity had problems (crash on startup) with the way DirectX switched resolutions, but setting the game and desktop resolutions the same avoided that. Similar issues have not been reporter for DD, but since the game is being minimized maybe having the game and desktop resolution the same will help.
You might want to try the game at 1024x768 anyway (at the very least you will have a much larger field of view... as long as text is still large enough to read).
[color:"orange"]occasionally the CDROM revs up, do you know why?[/color]
My guess would be a background program or something in Windows periodically checking the drive.
