FIXED.
Looking through the web I’ve found many pages talking about the bug but none explained how to solve the damn bug, not even mozilla 2006 posts had found a fix.
The bug (at least in my case) took place because I’ve set his directory (which is /.thunderbird usually stored at /home/user) in another memory storage, and from there I had created a “link” so when Thunderbird would have normally accessed his .thunderbird directory to load settings and etc it would have found the link which would have let him access the real directory which was in another place, I don’t know why but this is what made the bug appear, because once I copied the real directory back to its /home/user where it should be and deleted the “link”, it all went back to normal, and the error message did not appear again.
I hope this answer will help others to fix this uncommon but hateful little bug/error.
HOW TO FIX IT: make sure the .thunderbird directory (which carries all the settings, profiles, etc…) is where it should be by default (in my case /home/user), if you had previously moved it, put it back where it should be and it should fix the problem (at least in my case I’ve fixed it just like that).