Here is what I have found.  First of all, I have Ubuntu 10.04 with GLX-
Dock (Cairo Dock with Open-GL) installed on my system.  My issue was
caused when I installed the Cairo Dock add-on in Thunderbird 16.0.1,
then I right clicked on my Thunderbird icon in my GLX-Dock and selected
'other actions - fullscreen'

After that, I did not get the option in the GLX-Dock, or in Thunderbird,
to change it back to normal screen. What I found was that this changed
the screen size settings in localstore.rdf to the following settings:

<RDF:Description 
RDF:about="chrome://messenger/content/messenger.xul#messengerWindow"
                   width="700"
                   height="403"
                   screenX="0"
                   screenY="3"
                   sizemode="maximized" />

I then changed filename of localstore.rdf to localstore.rdf.old and
restarted Thunderbird.  Thunderbird created a new localstore.rdf file on
startup with the following default settings, which were correct settings
to eliminate the issue.

<RDF:Description 
RDF:about="chrome://messenger/content/messenger.xul#messengerWindow"
                   width="1024"
                   height="711"
                   screenX="0"
                   screenY="3"
                   sizemode="normal" />

note: screenY="3" on my system because I have a hidden panel on top that
is set to 3 pixels wide until I scroll over it. ScreenY would probably
be "0" on most systems.

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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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