I had the same issue after updating from Intrepid to the Jaunty beta.
When I enabled the GNOME compatibility option in CCSM the problem was resolved.
However, I believe this setting is new in Jaunty and should somehow be enabled 
by default when updating if both Compiz and Gnome are detected.
If this can't be done then it should be made clear that this option needs to be 
enabled when updating to Jaunty as it wasn't clear why Alt+F2 suddenly stopped 
working while other shortcuts such as Alt+F3 and Alt+F4 were still working.

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keyboard bindings partially ignored
https://bugs.launchpad.net/bugs/328679
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