I just noticed this when I was searching in Google. It appears that, whereever the color 0x00800000 appears (a dark green), content from other windows replaces it. To test this, I opened MSPaint, set the color to 0 for red, 128 for green, and 0 for blue and oddly, even with an all-white default image, I could see a moving picture behind it, from Virtual Dub (since I'm processing a video (compressing it and preparing it for YouTube) in the background). I can't take a screenshot of it because nothing shows up in the screenshot, as if nothing was wrong. Paint shouldn't have any support for dynamic, moving images, neither should Firefox for plain text (though for Firefox, it could be done using an animated GIF, but Google doesn't use animated GIFs...). Is this a bug with Virtual Dub, or is there something wrong with my configuration settings for video? That dark green is one of the standard 4-bit colors and is thus likely very commonly used.
Edit: Never mind, I found the problem. For some reason, Virtual Dub's settings, even though I backed it up, weren't saved upon reinstalling everything, causing my original settings to be lost. I found it in the preferences list, for "Use DirectX". There's a check there, by default, for enabling overlay....