(compiz version 0.6.0+20071008, on Ubuntu Gutsy)
When running compiz with the default settings on my computer, the Alt key removes focus from the current application, and therefore any application's keybindings using Alt do not work (notably, Firefox and gnome-terminal tabs).
I spent a great deal of time trying to find a cause and solution for this, and I believe I have figured it out. My keyboard has an odd layout that has caused me to remap my F1 key to Escape using a .Xmodmap file. Compiz has a default keybinding for Alt-F1. When Compiz has this keybinding for F1, yet no key can generate F1, it seems to get confused and steal Alt from all applications.
This is easily reproducible. Just run:
xmodmap -e 'keysym F1 = Escape'
and restart Compiz. If you have a compiz keybinding for Alt-F1, then you will notice that Alt removes focus from all applications.
This sounds like a minor problem that affects only people with strange setups, but it does seem that many people are having the same problem. For example:
Hmm, after finally figuring out the cause of the bug, I think I've found that the bug has already been fixed in later versions:
Further, it looks like it was a bug in Compiz Fusion, not Compiz. Sorry for the mistake.