[quote]The problem is pretty much just the inbox.  If I move all the emails to a tmp folder, and then move them back, the problem is cleared for a short while but comes back. [/quote]Why did you moved back the mails to inbox? After moving all emails back to inbox, you problems too are back. IIRC, the indexing works only in inbox and after having all mails back in inbox, mercury gets in trouble.

[quote]Since this is something that only recently started failing, I'm thinking that some spammer sent something that messed up mercury.[/quote]Possible but I believe not. Empty your inbox and one problem is gone.

I have been using Mercury mail for over 10 years now.  Recently, all of a sudden, without me doing anything to the server, it has started acting strange.  When I use Thunderbird IMAP client, a few of the OLDER emails in the Inbox will suddenly pop up as being unread.  I'm talking about emails that are 2-3 years old.  Its never done that before and thunderbird doesn't do it with the gmail and yahoo servers - only Mercury.

 Also, when I moved an email to another folder using thunderbird, it deleted it from the original, but failed to copy it to the new folder.

 Thinking the problem was with Thunderbird, I started up an old copy of Pegasus (v4.6?).  At first the problems seemed to go away, then I noticed something very strange.  The email that was highlighted in the listing, was not always the same one that was in the preview pane.  I double-clicked the listing email and the same wrong email came up in the new window.   Some email lines opened up the correct message body, but others did not.

 I immediately thought that maybe the Mercury indexes were somehow messed up.  The version of Mercury I have does not support re-indexing.  Its also not available in Pegasus for IMAP folders.  I found an external utility on this site that I was able to reindex all of the mail folders for that account.  It did find several errors in the indexes which it says it fixed.  That seemed to fix the problem in thunderbird and Pegasus for a while, but now its back.  

I was able to finally figure out how to delete Pegasus's cache which seemed to solve its problem of mismatched emails and headers.

Has anybody seen this odd behavior before and what was the solution?

What version of Mercury are you using? mbxmaint.exe (command line) and mbxmaint_ui.exe (graphical interface) should be included with the current release.

I've heard that messages in some cases could lose status flags when moved from a folder and back to the inbox. This and some other IMAP issues should be fixed in the upcoming v4.80, though.

How much emails do you have in inbox?
It is known to me, that Mercury (and perhaps Pegasus too) gets in trouble, if your inbox contains too much emails. After moving all old mails from the inbox to a folder outside of the inbox, the first part is done.
The second part would start with a shutdown your Mercury installation and using "mbxmaint.exe" (command line) or "mbxmaint_ui.exe" (graphical interface).  MBXMAINT can be used to move mailboxes, check and repair folders, and to compress deleted space from folders. To use MBXMAINT, simply run the EXE file without any parameters.

I'm using Mercury v4.72.

There are several hundred emails still in the inbox.  I'm afraid to move them because of the deleting after failed copy thing.  And also because of Pegasus showing the wrong header in the listing, I don't know for sure what I'm deleting.

I downloaded the mbxmaint tool and it fixed it temporarily.  

Right now its more of an annoyance than anything.  Should I just wait for v4.8 to  come out?

I think your problems get worse if you wait longer. If i remember correctly, problems in the inbox can not repaired. I would move all mails from the inbox in a new IMAP folder, shutdown Mercury, copy the folder "Mercury\mail" on an external drive as backup and start the mbxmaint tool.

I'm still getting this bug.  Pegasus and Thunderbird both respond to the bug, but in different ways.  In response to NEW mail, thunderbird highlights an old email (sometimes years old) and marks it as unread.  While Pegasus displays the heading of the new email(s) but will get a pop-up IMAP error when trying to read some, but not all of them.

I have reindexed all of the folders in the mail directory and it usually fixes it for a short while, but then it comes back. So I think the reindexing program is working, but something is messing it up again.

 Is there any way to delete all of the mercury indexes and let it simply rebuild them from scratch?

 The problem is pretty much just the inbox.  If I move all the emails to a tmp folder, and then move them back, the problem is cleared for a short while but comes back.

 Since this is something that only recently started failing, I'm thinking that some spammer sent something that messed up mercury.

I think it would be a good idea to start by upgrading to version 4.74 of Mercury. There are a number of IMAP fixes in recent versions.