Ah, you used my suggestions over there. ;-)
I agree that the account may have been hacked. A lot of that with Hotmail and Yahoo lately. They don't change your password, just use the account. Change your password.
Also, for the duplicate downloading, your popstate.dat file may be corrupted. Here's the info on that which I also regularly post on Mozillazine.
First, move all of the messages you want to save to another folder outside of your inbox. You shouldn't store them there anyway, but also that will make this process easier.
With Thunderbird closed, go into your profile.
http://kb.mozillazine.org/Profile_folder#Thunderbird
If you are using Windows, before you try to find your profile, you need to set "Windows to View hidden files and folders" and to not "Hide extensions for known file types". See this for easy instructions for how to do this:
http://spywarewarrior.com/viewtopic.php?t=272
Now, find the file popstate.dat which is in your Mail>*account* folder for this account and delete it. This file is Thunderbird's memory of what it has downloaded and I suspect that it is corrupted. When you reopen Thunderbird and get mail for this account it will download everything from the server one more time. Clean up by deleting all the repeated mail in your inbox. Compact your folders again (and at least weekly from now on). This should fix the problem.