Is there a Repair function?

My Mail.app is not working properly.
Lots of times, after I view mail, it moves back to "unread" status again.
Whenever I reply to a message I get the reply arrow, but clicking on the arrow no longer takes me to the reply message (double clicking simply takes me to the incoming message). In fact clicking on the arrow does nothing.
The application clearly has difficulties. Is there a simple maintenance tool or is anyone here versed in the dark-arts of Mail.app repair?
Thanks in advance.
pBook 12/1.5mhz   Mac OS X (10.4.2)  

Jules,
There are quite a large number of other topics about problems with flawed and/or failed conversion of mailboxes from earlier versions of Mail, to Tiger, and steps to address those problems -- See also:
http://discussions.apple.com/thread.jspa?threadID=413196
and
http://discussions.apple.com/thread.jspa?threadID=340466
and the underlying support document at:
http://docs.info.apple.com/article.html?artnum=301315
If you can remove all leftover files -- but only after checking the size of mbox files versus Messages folders, or being otherwise satisfied that you are not missing any pre_Tiger email messages -- then the next step may be to force Mail to re-index all the mailboxes.
There is quite a potential for leftover, unnecessary files from each previous version of Mail.
Ernie

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