I'm having a similar problem with both Thunderbird and my Blackberry. Thunderbird (on two different machines) repeatedly re-downloads and reindexes my inbox. The Blackberry downloads the same subset of messages that are in the inbox over and over. It's playing havok with the blackberry. Thunderbird seems to deal with it, but it's annoying to have to wait for it to finish it's process all the time.
I've been using this setup (Thunderbird and Blackberry) for at least a couple of years now and have never experienced a problem like this.