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Go to System >> Preferences >> CompizConfig Settings Manager >> General Options >> General and uncheck the option Unredirect Fullscreen Windows

P.s.: this might not improve flash performance for all Ubuntu / Linux users, but will most definetly help some...

You may also want to read (regarding Flash issues and Linux):
Speed Up Flash and Firefox in Ubuntu Jaunty
How To Fix Full-Screen Flash Videos in Linux & Firefox (or Swiftfox)

[via phyx]