I recently migrated to Thunderbird 3.0.3 There is a specific problem with Thunderbird that I have seen at times. Ever faced a problem of loosing your mail data and accounts after migrating to new Thunderbird? Thunderbird stores data under directory named .thunderbird in your home. But maybe just in Ubuntu or some versions of Thunderbird store it under directory named .mozilla-thunderbird. So if after installing a new Thunnderbird and restarting it, if you are not able to see your e-mails, it might well be the problem of directory names.
To resolve, try renaming the directory (Whatever applies to you),
> mv .mozilla-thunderbird .thunderbird
or
> mv .thunderbird .mozilla-thunderbird
Restart your Thunderbird and now you should be able to see your e-mails.
I have mostly seen this problem when I install Thunderbird externally i.e. not through package manager. By installing I mean simply extracting it to /opt and not doing "./configure make install"
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