Mail junks legit archived emails

Everyday now I find a (randomly selected, as far as I can tell) email in the junk folder. It seems that Mail is somehow picking one such email from a mailfolders and tossing it into the Junk folder with the actual junkmail. This forces me to open & check the junk mail folder constantly -- though happily the hijacked mail is always at the top of the folder (I arrange my folders by date received).
Has anybody come across the same aberrant behavior? And found a way to teach Mail not to eat its archives?
Many thanks fior any advice,
Pierre

If you're talking about messages that were received some time ago (i.e. not incoming messages), this kind of problems are caused by some index corruption.
Verify/repair your disk first (not just permissions), as described here:
The Repair functions of Disk Utility: what's it all about?
After having fixed all filesystem issues, if any, and making sure that there's enough space available on the startup disk (a few GB, plus the space needed to make a backup copy of the Mail folder), try this:
1. Quit Mail if it's running.
2. In the Finder, go to ~/Library/Mail/. Make a backup copy of this folder, just in case something goes wrong -- e.g. by dragging it to the Desktop while holding the Option (Alt) key down.
3. Locate Envelope Index and move it to the Trash. If you see an Envelope Index-journal file there, delete it as well.
4. Open Mail. It will tell you that your mail needs to be "imported". Click Continue and Mail will proceed to re-create Envelope Index -- Mail says it's "importing", but it just re-creates the index if the mailboxes are already in Mail 2.x format.
Note: For those not familiarized with the ~/ notation, it refers to the user's home folder, i.e. ~/Library is the Library folder within the user's home folder.

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