I did not have this issue with Ubuntu 11.10. Well, to be clear, I did, but it was easily remedied with compiz workarounds.
I have tried both the propriety and open source ati drivers, and the intel HD 3000 (as far as I know) should be part of the Kernel already. So I am pretty much 100% stumped given my general lack of Linux knowledge. I really enjoy this OS, would hate to have to return to Windows (read: HATE) because of something as trivial as video playback.
Lenovo Thinkpad Edge e520 Intel HD 3000/AMD HD Radeon 6630m
Ubuntu 12.04 64bit.