[Eris]

I'm seeing this same problem (the lack of window focus), most especially with Firefox and Thunderbird; have also seen a hint of it (but not so consistently) with Adium. It doesn't happen when I use ctrl-arrows to go to another screen and then back, but does happen when I use command-tab.

Hard to tell if it's an OS-side bug or a Mozilla bug where the applications aren't handling things in just the right way, I guess.

I don't click to get focus, though, I just use command-` which switches windows and focuses just fine. Whatever happens, must not remove hands from keyboard!