This is all very interesting. I had no idea when I started this thread the number of others that are suffering this same problem.
Sounds like it might be worthy of looking in to.
I am unable to switch to anything during the time this occurs and basically stuck until it simply stops. ALthough in clicking around, I discovered last night, of all things, right clicking on PC at the title bar for some reason seems to reduce the time and in a few cases, stop it completely. What I've noticed throughout is once the main stuff stops, there are still a few short seconds where just the menu in top left flutters some more before AE is usable again.
Maybe others can try my right click and see if you have same reaction.
Eric