This is a very nuanced problem concerning video issues.

I've been using Latex, Compiz-Fusion's Annotate function, and gtk-recordMyDesktop to make math videos on YouTube. But, today, all of a sudden I have this problem that makes it impossible to make the videos. Whenever I clear the annotation, it doesn't clear in the video. I haven't changed anything that would cause this to happen, so I can only imagine that it has to do with a recent update.

The problem appears to be in Compiz, not gtk-recordMyDesktop, because I have the same results with screencast-o-matic.

Does anybody have any idea how to fix this? I tried using Ardesia instead of Compiz's annotate, but it's so buggy that it's pretty much useless.