I had a similar problem with Thunderbird Greying out and than everafter displaying some of my account setup but none of my mail. On looking at the mail storage links I noticed that Ubuntu made a huge change that broke all my folder allocations. I use Ubuntu at home and Portable Thunderbird at work where I use a Windows box. So I store my mail on the portable drive with the PortableApps on it so that I can carry it from home to work and back again. In both systems, Thunderbird points to the same directory on that portable drive. Ubuntu has changed the way this works as follows:
Instead of: /media/drivename/
In 12.10 it's: /media/username/drivename/
Which means I had to manually edit every folder location in my Thunderbird settings. What an unmitigated pain! However it fixed my problem.
I hope this helps.