Problem with multiple same emails - thinking of clean reinstall

Hi. My OS is windows vista home edition and I am using Thunderbird version 31.0. My email provider is MSN.
When thunderbird checks mail, Instead of receiving one copy of an email, I am sometimes getting two and even three copies of the same email. They all have the same date and time. I have tried some suggestions including deleting .msf and popstate.dat files and also making sure that the server is not set to keep emails there. This fixes things for a day and then I am back to getting multiple emails. It's annoying.
I am thinking about doing a clean reinstall of TB. I have the mozbackup utiility and I am going to back up emails and contacts. As far as uninstalling thunderbird completely goes, is there an instruction page for that? Does anyone think this will help?
Thanks!

A note for the future....
Files:- Are rebuilt by right clicking a folder, selecting properties and then repair. It is easier that digging into the file system. The other "index" you refered to with no extension is not an index, it is the actual mail. Inadvertently deleting local copies of mail not on the server can be something of a disaster. Right clicking the folder and selecting compact will clear corruption there. But it may well get rid of corrupt mail as the MSF files are what is used to display lists in Thunderbird.
This add-on make managing duplicate messages much easier. https://nic-nac-project.org/~kaosmos/index-en.html#recDelMsg

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