How to (re)enable YouTube videos on Safari with Flash plugin 10.2?
I had this problem while running ClickToFlash 1.6b9 (the original general browser plug-in, not the Safari 5.x extension). Even with ClickToFlash  disabled via the checkbox in ClickToFlash's preferences, it still happened. I ended up dragging the ClickToFlash plug-in out of /Library/Internet Plug-Ins/ and restarting Safari, and it went away.