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1b1ed1a
(Get the code!)
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.