Maybe it's just your color depth? I tried mine in 128 colors and it worked fine for an hour but then started to glitch a little at 1024x768. I'm now running it 640x512 and 256 colors and it's rock solid (and looks awesome too!)
Perhaps, buy back before the config tool came out I put mine in 256 color mode and stress tested it pretty well with various programs... I'm pretty sure it does not occur.
Not to say my A1200 does not have other issues

I think it has failing caps or something that cause flaky behavior with the IDE controller.