I am experiencing exactly the same. It is really annyoing!
I don't use Firefox, so I don't know anything about that. But in Thunderbird it 
seems to happen almost every time I have new mail and want to read it. I can't 
open my Inbox and I am unable to click on it in that case. I always have 
Thunderbird minimized and I maximize it to read my new mail. I am using Ubuntu 
11.04 with Unity and Thunderbird 3.1.9. 
It may be important that I use the Thunderbird Indicator extension and that 
after getting new mail notifications I maximize Thunderbird using the Link in 
the indicator.

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https://bugs.launchpad.net/bugs/772650

Title:
  randomly gap appear between GUI and cursor on firefox and thunderbird
  maximized

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