I've a sneaking suspicion this is a kernel issue rather than X itself.
Not sure exactly how to isolate it, however here are some things to look
at:

* dmesg
* /var/log/messages
* lsusb
* lshal

Any errors or changes in those files before/after one of these focus
losses would help pin down what's going on.

-- 
major window focus problem in X
https://bugs.launchpad.net/bugs/229123
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