It's definately an Thunderbird indexing problem. I have the same problem occur regularly with Thunderbird on Windows (2.0.0.19). Seems to occur mostly (for me) with IMAP folders that are set to be available for offline use. Deleting the .msf files, or selecting Re-index from the folder properties fixes the issue, but is a real pain because the re- indexing removes all of the tags I use to categorize each email.
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