IMAP Deleted Messages AND Unread Messages

I've read quite a few threads about two seemingly persistent problems using Mail and IMAP servers: a) Messages deleted within Mail "reappear" in the client's in-box, and b) messages read (and marked as read -- no blue dot) "reappear" as unread messages (this latter problem occurs for me, even if moved to a folder on my IMAP account). I have to admit that I've gotten lost in the twists and turns of these discussions and I'm reluctant to start trying things that may make matters worse.
I've tried to extract the right things to do here -- and, so far, only have checked that I am indeed saving deleted messages on the server.
May I ask: In summary terms, are there a few standard fixes for making deleted messages go away and read messages stay that way? Thanks!!
PB 12"   Mac OS X (10.4.7)  

I'm using Mail 2.1 (752/752.2) talking to a Cyrus IMAP server running on the same machine. Messages are kept on the server. I have a GnuPG mail plugin. Ever since the last update of Mail I've had the problem of random "read" messages returning to the "unread" state, and not just in INBOX, but in other folders, all on the server. I've read them, did "Synchronize" and they soon show up as "unread" again. I've read them, quit Mail, restarted Mail, and they are "unread" again. Sounds like what other people are seeing.
So I wrote a program that talks directly to the IMAP server to see what it thinks about the "read" status. Sure enough, messages that have a sitcky "unread" state do not have the IMAP "\Seen" flag set. In other words Mail is not setting this flag for some reason. (I've check this several times, before and after Mail is supposed to mark a message "read," after quiting Mail, etc., and the "\Seen" flag is never set.)
If I use my prober program to manually set the "\Seen" flag on a message, then it stays "read." That message never again pops to the the "unread" state; however, random new messages get stuck in the "unread" state. So far the only way I have been able to mark these sticky messages as "read" is to talk directly to the IMAP server.
I believe this strongly indicates the problem lies in Mail itself and not the IMAP server. I believe there was some regression with this new version of Mail because I've never had the problem before. To conclusively prove Mail is at fault, though, I would have to eavesdrop on the communication between Mail and IMAP.
--Mike Zuhl

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