Message count in Mail doesn't agree with emlx count in Finder

Question

I was checking a recent backup and I noticed the number of .emlx messages in:
~/Library/Mail/[email protected]/INBOX.mbox/Messages
did not agree with the message count Mail (Version 2.1.1 (752.3)) gave in the title bar for the Inbox of that account. In fact, the number of files in:
~/Library/Mail/[email protected]/INBOX.mbox/Messages
was almost 1000 and the count given in Mail was about 175. Of course, this is not good. My immediate reaction was to rebuild that mailbox. I did so and now the numbers agreed, but there were 100 messages in that Inbox that were not there before (messages going back several months that had been filed away or deleted long ago). In addition, a number of messages that were read before, were now marked as unread.
Being rather worried about this (I heavily depend on Mail), I proceeded to check several other mailboxes and found that many of them had .emlx Finder numbers that did not agree with the count shown in Mail. Should all these mailboxes be rebuilt?
Finally, for several of my mailboxes, when I rebuild them, huge numbers of messages that were read before are then marked as unread. If I mark those messages as read and rebuild the mailbox, the same thing happens again -- they are unread. This doesn't sound normal either.
Can anyone give me some insight as to what is going on here with Mail and how to fix these issues?
Thank you.
2.16 GHz MacBook Pro   Mac OS X (10.4.9)   2GB RAM, 7200 RPM HD

Answer 1

All I can tell you is that, rather than rebuilding each and every mailbox, you’d better re-create the entire index. That won’t fix the read/unread issue, though. Apparently, Mail sometimes fails to permanently store the read/unread status in the *.emlx file itself, and hence, that information is lost every time the mailbox is rebuilt or the index is re-created — don’t ask me why.
Verify/repair the startup disk (not just permissions) first, as described here:
The Repair functions of Disk Utility: what's it all about?
After having fixed all the filesystem issues, if any, and ensuring 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. This is where all your mail is locally stored.
3. Locate Envelope Index and move it to the Trash. If you see any other “Envelope Index”-named 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. That is, ~/Library is the Library folder within the user’s home folder, i.e. /Users/username/Library.