Mail: smart mailbox contents disappears/search doesn't work & fix is only temporary

Since installing Mavericks (including the Mail update), the contents of my Smart Mailboxes disappears (the Mailboxes themselves are listed, there's just no content) and my ability to get results from Search within Mail disappears. 
I have done a lot of searching here and via Google and read other people with similar problems.  I have done the usual magical stuff: resetting permissions (including the version that involves the command "resetpassword"), deleting caches, etc. - but to no avail.
Spotlight clearly knows about all this mail, because I can find it with HoudahSpot, which uses the same database, but somehow Mail is not able to read what Spotlight knows.
Now there is a commonly recommended fix, which is to go to Terminal and type some version of:
mdimport ~/Library/Mail/V2
This works (as does reindexing the entire disk)!  But only for about a half-hour to an hour, at which point Mail reverts to its previous state.  Running the command again works again, but once again the cure goes away shortly after.  Once again, the Smart Mailboxes are empty and search in Mail stops giving reslts.
Can anyone suggest a real, permanent solution to this problem, besides switching to another email program?

Okay, I think I understand better now.  So I just ran a test, by creating the following rule:
I specifically chose an address (obviously not the one shown) that I had a message from in my Inbox, and a word that was present in the subject line of several messages in my Inbox.  When I ran this rule on my Inbox, it copied exactly the messages I would have expected into the test mailbox.  Are you seeing different behavior with the same rule, or is your rule constructed differently?
If the difficulty is with running the rule, note that (as I said earlier) rules only run automatically on unread incoming messages.  It won't run automatically on existing messages or on messages on an IMAP mail server that you have read on another device using (in which case they will have been marked as read).  If you need to run this in such conditions, you'll have to either run the rule manually or run it via an AppleScript or something similar that is somehow (via something other than Mail) made to execute at certain times/intervals or under certain conditions.
And you're correct, a smart mailbox would be totally inappropriate for what you're trying to do!  It would behave exactly as you guessed.

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