Missing mail - disappearing mail

after upgrading t 10.4.6 mail.app has suddenly exhibiting some very strange behavior;
i watch emails coming down from server, and then i go to read some of them - even clicking on one for instance _ and it disappears. fortunately i am able to log into my mail server via control panel and see the mail.
the other thing is there are a number of folders that show that messages (apparently unread) are in the folder, however when clicking on the folder name, the folder is empty.
doing a "get info" on the folder shows the messages that are on the server related to that particular POP account.
also, i have noticed many topics related to missing email, and loads of posting reads, but NO responses. what is up with that?

Problems appearing as a result of updating the system software are usually a consequence of the update not being done properly. Read the following article for guidelines on how to properly install system updates:
Installing software updates
In particular, you should consider verifying/repairing your disk (not just repairing permissions):
The Repair functions of Disk Utility: what's it all about?
You may also want to consider reinstalling the update using the combo installer:
Mac OS X 10.4.6 Combo Update for PPC
That said, your problems might very well have nothing to do with any of the above. If I've understood it correctly, your problems are not the result of upgrading from either Jaguar or Panther (i.e Mail 1.x). That is, either you started using Mail in Tiger (Mail 2.0) or you didn't experience any problems when upgrading from Mail 1.x, right?
If the above is correct, try this:
1. Quit Mail.
2. In the Finder, go to HOME/Library/Mail/. You may want to 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 the Envelope Index file and move it to the Desktop (to be deleted later if this solves the problem).
4. Launch Mail again and let it finish re-indexing everything -- it says it's "importing", but it's just re-creating the Envelope Index file.
It could also be that you have problems with rules, but try the above first.

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