Mail Has Been Broken in 10.4.5

Question

I have the following complaints about Mails inability to function properly, and more so since upgrading some machines in our office to 10.4.5.
We are in business and rely on email. Mail is becoming useless. We want to continue to use Mail, but are being stymied by its continual lack of performance and reliability.
1. IMAP: is very unreliable. Sometimes it works, sometimes it synchronizes, sometimes it doesnt.
2. Junk: With the upgrade to system 10.4.5 from 10.4.4, the junk mail filter is broken. Does not filter junk and does not remember mails that I mark as junk. Ive reset the junk mail filter but it doesnt work. I mark mail as junk, yet mail from the same junk mailer appears in my inbox again and again.
3. Legitimate mail is sometimes routed automatically to other folders, or to the trash.
4. Spell check has become less reliable or not functional at all.
This isnt a problem with one computer, but with my entire office, especially but not limited to those that have upgraded to 10.4.5.

Answer 1

I'd like to thank Ernie Stamper for his patience and helpfulness on this issue of mbox problems after the latest upgrade to OS 10.4.5. While I can't point now to the specific posts where my strategy was learned, I've solved the Mail App issue and am back in business. Perhaps my strategy won't work for those with lots of e-mail, but I've always had a strategy of Save As anything of value and trashing the rest with the exception of half a dozen 'active' mailboxes which seldom have more than ten items in them.
Solving the Mail crash was simple enough. I removed the Mail folder from my user library to the desktop. I trashed the com.apple.mail.plist. Relaunched Mail App and entered my accounts and configured it once more. I then used...
http://www.cosmicsoft.net/emlxconvert.html
...to convert the old mboxes to a normal mbox file. Strangely the import function of the Mail App wouldn't work on it's own mailbox format from the day before the 10.4.5 update but would import 'normal' mbox files. Once imported and a little moving files around and I'm good to go!
Thanks again Ernie.
G4 1.5GHZ, Rev.A iMac, Mac IIsi, Mac Plus   Mac OS X (10.4)