I had the same problem after upgrading from 9.04. I needed to left-click
to make the top panel disappear. I didn't use a custom compiz profile.
I just switched from 'extra' to 'normal' and the problem dissapeared. I
switched back to 'extr'a and the problem remains solved.
** Changed in: totem (Ubuntu)
Status: New => Confirmed
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Gnome Panel not hidden when going to fullscreen
https://bugs.launchpad.net/bugs/465933
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