I have also been hit by this one. I had upgraded from Intrepid to Jaunty
shortly after it was released. The bug did not surface till 3 - 4 weeks
ago after an upgrade. I am now at the latest Jaunty and still seeing
this problem, which is solved by logging in, and logging out immediately
after system boot.

Just to add a possible pointer to what some are reporting, the bug did
surface shortly after I had installed a Genius Tablet, but I did not
notice it immediately. So, this is just one more data point hinting at a
link to the use of extra input devices.

I have now downgraded to hardy's xserver-xorg - and all is fine (except
that the xserver consumes all the CPU on one of my cores :-). I can live
with that though till the problem is fixed.

Could someone please promote this bug to High Importance? It is
insidious - and seriously dented the Ubuntu experience for my spouse and
kids. Eventually it did get promoted when it originally appeared in
Intrepid.

-- 
Focus gets stuck to a window - impossible to select other windows
https://bugs.launchpad.net/bugs/362359
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