@davewill: In Vista I've experienced something like that with Outlook when I had the Outlook gadgets running on the desktop. The content and the chrome got all wonky and you could do nothing but kill the app and restart it. I reported it to Microsoft via the forums and they said it was a known problem with the APIs that the gadgets were using. Like your experience it would only happen when the window was inactive.
Just this week my debugging broke for web stuff in VS (at least with Cassini). If I manually attached the debugger to the process when the breakpoint was hit VS would go wonky just like my past experience with Outlook. I'm sure it's totally unrelated but an interesting similar behavior none the less.
Video driver updates fixed neither of these problems unfortunately.