I also experience the same bug with my Microsoft Intellimouse Explorer
for Bluetooth mouse and also with my MacMice bluetooth trackball.

I tried Matt's suggestion and changed my session to my Failsafe GNOME,
but that did not help and I kept losing focus for my mouse clicks.

The symptoms are exactly the same as above, but I have noticed that I
can regain focus temporarily back by doing following:

- I click a new window or some other element such as a button / slider / text 
area.
- After that the focus is lost to the previously focused element.
- I can regain focus back to the active window by right clicking on the 
previously focused element (if possible).
- After I close the right click menu after that, I have focus temporarily until 
I click a new element.

I am using currenty Edgy Eft, but I have experienced the same focus
problem with my Bluetooth mouse and Bluetooth trackball also in Dapper
Drake.

-- 
USB mouse clicks seem to go to /dev/null
https://launchpad.net/bugs/24348

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