This may seem simplistic, but it worked for me. All I did was rename (not copy) the numeric part of the prolile folder name and in the "profile.ini".
I changed my original profile folder name from...
97234.default (your number part of the name will be different)
to...
12345.default
I followed with going up one level and editing the "profiles.ini" line from...
Path=Profiles/97234.default
to...
Path=Profiles/12345.default
I saved the "profiles.ini" and fired up T-Bird and My mail was back! The only caveat was I had to re-install all my Add-ons. I am still working on how to make them re-appear.
Hope this works for you too!
Update...I did some more experimenting and I found the following...
-=o=- I was able to rename the profile folder/path entry to anything I tried "jhasdjdf034ai7uha4n80q734uih80qhcv8734hn.default" this was just random jibberish and it worked just fine. I also tried using a single character or number and that worked too. It seems that any matched string will work, but I put mine back to the original, just in case.
-=o=- I also found that to restore all my Add-ons all I had to do was go into the Tools >> Add-Ons and select any one of them and then re-select the same one. I exited out of Thunderbird and re-opened it to find all my extensions back and working perfectly. Please note it was not necessary to select/deselect each one.
-=o=- I was also able to duplicate the dreaded "Thunderbird is already running..." error message and I was able to fix it. The fact is that Thunderbird was
not running. This is why you can't go into the Processes and turn it off. It isn't there. It is not running.
I was able to reproduce the error at will by making any kind of incongruent change in the number part of the "Path=Profiles/54321.default" line in the "profiles.ini". Like making it Path=Profiles/5432.default"
WHILE Thunderbird was running. I wasn't able to make the change like this to the "54321.default" in the profile follder since it was being used.
It appears that when Thunderbird is opened it checks to make sure that something in the "54321.default" is not open (maybe the folder itself) and it checks against what is in the "profiles.ini "Path=Profiles/54321.default". I really don't know for sure, but what I do know is if these two are not matched then Thunderbird assumes it is running because it appears to T-Bird that the profile folder is not available and produces the "Thunderbird is already running..." error. The good news is that it is easy to fix!
You need to make the "Path=Profiles/54321.default" line in the "profiles.ini" and the "54321.default" folder name match and it will work AFAICT. As a final experiment I renamed them both to "mouser" without the ".default" part and it worked just fine.
-=o=-
Conclusion - The reason this error appears is somehow the profile folder name or the "Path" information becomes corrupt in memory and when you try to open T-Bird it throws the error. I am guessing it has to be in the memory or registry(?) because I never was able to see any visual corruption other than my own intended discrepancies. Since the corruption has occured before I figured this out, I was not able to verify if there had actually been a name/path change. If any of you are experiencing the "Thunderbird is still running..." error, I would be interested to have you look at the profile folder name and the "Path" line in the "profiles.ini" and report back if you did or did not see a discrepancy.
Your mileage may vary, but it was completely consistent for every experiment I tried. I am not a "Guru" or hacker. I just tried something and it worked for me. Maybe it will for you too!
Lastly, if you have any kind of corruption with T-Bird that makes it unusable, regardless if you get "Thunderbird is still running..." error, please try the renaming as outlined above and post back with the results.
Hope this helps someone.
<edit> spelling and re-formatting for readability</edit>