I'm having this issue and I can't get the stupid window to stop popping up. I'm completely unable to do anything in my timeline. I CAN click on one of the menu items at the top if I'm fast enough and I've tried purging "all" as well as cache and video memory (I've tried them all basically) and it makes no difference. The window just pops up again immediately. I've made my cache larger (way larger than should be needed) and nothing comes of that either. Why does AE have an error that prevents you from doing anything to fix it? I've closed the project, quit AE and restarted, to no avail. Am I going to have to trash my entire project and start over? Frustrating!
Well, I solved it by using the menu command "Lift Work Area". I had never used it before but it removed the layer that was causing issues. Luckily it was one that I could just place right back into my timeline with very little work to redo. I have no idea if this was the proper way to do it or not, but it's pretty frustrating that it had to be done at all, and just as frustrating to discover that I couldn't find a solution ANYWHERE.
So basically I'm posting this for anyone else who winds up in my situation and can't find any real help.
Adobe: you've got to fix problems like this. Seriously. I love After Effects and have been using it for several years now. Admittedly I've never encounted this before, but you can't have a window pop up indefinitely, preventing you from doing anything about it. It's amazing that I was able to do anything at all. You've got about a fourth of a second to click on the menu bar before the next error window pops up, and a fourth of a second might be a generous estimate.