For what its worth, I have an Nvidia card and am running Ubuntu 12.04: Chrome's Flash plugin does not work very well on the latest dev build; it has some weird issue with playing flash at double speed or something. I had to switch back to Adobe's flash plugin until this issue is resolved... This could potentially be hardware specific in my case, but, just wanted to let others know that Adobe's plugin still works.
I've experienced the same issues. Some sites, like Udacity, is borderline broken for me. I applaud the effort to move off the Adobe plugin, but it's important to remember that to the end user, we just really care about how well it works. In the meantime, I've gone back to using Firefox.
I had that same problem start occuring too, after a recent update. 12.04 x64, but with Intel HD3000 and no discrete GPU. However, a subsequent update seems to have fixed it, it's gone now.