Well, it seems that courier-imap presents threads to the client in the order of the filenames. So if you move a message that starts a thread into a another folder and back this thread will be shown as the first thread, even if there are threads that were started after this message arrived. This might be also a client problem in sorting the threads, but renaming the message file changes the sorting.
Moving a message between folders also renames the message file, so both statements can't be true.
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