Hey there...I noticed the same thing after installing Safari 3.0 beta. From what I've read, others have noticed this as well as a "lag" in iChat.When replying to a message in Mail 2.11, the reply window doesn't come up until I move the mouse. If I just click reply, nothing will happen it will appear frozen. Then move the mouse and voila, window appears.
I'm pretty sure this started happening before I installed the OSX update but I didn't catch what the problem was...I thought it was just being slow because my inbox was too big so I trimmed it down.
I ran the software update and installed the 3.0.2 patch, which seems to have solved the problem.
If you've got the new browser installed, this may solve your problem!