I am having the same issue. After updating to 10.6.5 all my tools in most adobe programs cease to work. Also, all my quicktime codecs in After Effects magically disappeared...its not a single instance of this, many people are experiencing the same thing. However, not EVERYONE is experiencing it, which seems odd. I talked with a Senior Advisor on the Apple help line today. He said there was a program that is packaged into 10.6.5 that switches keyboard controls for that program, and the Adobe Suite doesnt like it. Thus the strange phenomenon where it looks like the alt key is pressed and you cant do anything.
Re-installing my OS has been the only resolution thus far. Unacceptable.
I found a temporary solution to this problem. Photoshop CS5 thought I had the CONTROL key held down, so I wasn't able to select anything, etc. This app will force the modifier keys up, temporary solving the problem. Hey Apple, based on the threads I've read, this is problem is affecting many apps in addition to Photoshop, so please fix.