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Sometimes Thunderbird has problems if it’s trying to reference a mail profile that’s in the wrong place. You need to locate the following file: C:usersyourusernameappdataRoamingThunderbird. (Note that Appdata is a hidden file.) There should be a text file there called profiles.ini. If this is pointing to an incorrect profile location, then Thunderbird will tell you there’s another copy of Thunderbird running. The file opens with notepad, and the text gives the path to the profile. Check to see that the line “Isrelative=1” is there — that should prompt Thunderbird to create a profile in its default location. If “isrelative” is set to 0, it will look for the profile somewhere else. If it doesn’t find it, it won’t open. Don’t know if that’s your problem, but it can cause that message.

I’m assuming that you are upgrading from a previous version of Windows. The profile.ini and related files in Windows 7 (& Vista too I think) are kept in the path noted above. If you place it where it was in XP and earlier versions of windows under
C:UsersxxxAppDataLocalThunderbirdprofiles.ini It won’t work. (xxx is yourusername)
This link may help.
Thunderbird already running