Same here.
During upgrade from 13.04 to 13.10 I had some problems in compiz/3d 
acceleration/desktop elements (panel disappeared) and so on.
I was using thunderbird and it remembered the "wrong fullscreen" position.
After some tricks and updates my desktop was ok but thunderbird always started 
fullscreen, no matter what.
Editing the localstore.rdf from:
                    width="1539"
                    height="847"
                    sizemode="fullscreen" />
to 
                    width="800"
                    height="600"
                    sizemode="normal" />
solved the problem.
Thanks all for the hints

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https://bugs.launchpad.net/bugs/196058

Title:
  Thunderbird starts in a full-screen mode and cannot be restored

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