Have you ever used Ubuntuzilla to install thunderbird. We use 
~/.mozilla-thunderbird as the dir with profile and the Ubuntuzilla  uses 
~/.thunderbird, as far as the versioning is with thunderbird there is a bug on 
it already. 
See bug #156607 for version number bug. 
I have been gone for a few days but as far as i knew we were not gone change 
the ~/.mozilla-thunderbird to ~/.thunderbird just yet. Please make sure you 
have ~/.mozilla-thunderbird
I had a user come to me the other day with this same issue and it was caused by 
Ubuntuzilla , Please confirm that you have used it or you made ~/.thunderbird 
and used it.
IM closing this bug due to it not being ubuntu packages fault as our packages 
still use ~/.mozilla-thunderbird as the dir for profile, As for version bug see 
bug listed above. 

** Changed in: mozilla-thunderbird (Ubuntu)
     Assignee: (unassigned) => Mozilla Bugs (mozilla-bugs)
       Status: New => Invalid

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Thunderbird package update lost my profile
https://bugs.launchpad.net/bugs/156707
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