I also just updated to firefox 3.0.6, and I am also affected by this banner. 
The follwoing things didn't help:
- File -> Quit
- click 'Restart' (Firefox actually restarts, but banner does appear again)
- sudo killall firefox

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∞Your browser has been updated and needs to be restarted.
https://bugs.launchpad.net/bugs/289365
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