OK GUYS - If you're still having problems, try these suggestions. I've had the same issues. DISCLAIMER: It worked for me, but there are too many variable to guarantee it will work for you too!!
***IF POSSIBLE: Before going any further, access your email accounts via webmail and set each of them up for IMAP. If you have an email provider that DOESN'T provide IMAP, other than maybe an exchange server at work, get a new email provider or web host. You'll be glad you did down the road. Plus it's just better. And it's like having an automatic SuperDuper or TimeMachine backup for your email.
FIRST: Download an app of your choice that will run maintenance on your computer, specifically one that will do a) cache cleaning, and b) rebuild Mail.app mailbox index. There's an app called Maintenance which I use. Think you can find at versiontracker(dot)com. These apps may take a while the first time, but that's a GOOD THING! Don't waste your time rebuilding your mailboxes via Mail.app, at least not yet.
**Maintenance.app will very your disk and repair permissions for you. However, if you use another app, ALSO REPAIR PERMISSIONS and run a Disk Verification via Disk Utility.
SECOND: Make a folder on your desktop called MAIL *****. Nothings special to the name, just might help your frustrations.
THIRD: We need to manually save your MAIL.APP file such as RSS Feeds, To-do's, etc. Using the finder, go to /Users/your user/Library/Mail (this isn't the Mail Folder in your user's Library)
Now, simply drag the contents of this folder to the MAIL ***** folder on your desktop! Be sure not the drag the actual Mail Folder here...just it's contents.
While your at it, if you can, delete the contents of your Mail Downloads folder at
/Users/your user/Library/Mail Downloads
Just to be safe, I'd make a copy of the MAIL ***** folder somewhere OFF of your main Hard Drive.
FOURTH: Now, simply go to: Macintosh HD/Library/Mail/AccountTypes. Delete the contents ONLY of the AccountTypes Folder. NOT THE ACCOUNT TYPES FOLDER.
FIFTH: Place your computer (hopefully it's a laptop) in your freezer for 24 hours. Ok just kidding!
Seriously, SHUTDOWN & RESTART YOUR COMPUTER > Don't just log off and back in or simply restart. Use the shut down function and then restart. COMPLETELY.
Almost done!! From here you have some options. I'll list them but don't have time to get into detail. Truthfully, if you're not sure how to work these options, I'd just stop here and hit up the Apple Store or call AppleCare.
OPTION ONE: Reinstall Mail.app via your Leopard DVD and an app called Pacifist (versiontracker). You're not reinstalling the whole OS.
OPTION TWO: Restart Mail.app and proceed. It should act like you've never set up any accounts.
OPTION TWO A: You can Import Mailboxes via Mails Import feature, but if this doesn't work, you'll have to start all over for any option to work.
IMAP USERS: Use this option and simply let the IMAP do what IMAP does, sync your email back to your computer from your mail server.
OPTION TWO B: (POP3 users only) You can manually drag the following folders and files from the MAIL ***** folder back to their original home on your hard drive (remember above):
Your actual mail account folder (should start with IMAP or POP)
Mailboxes
Message Rules.plist
The rest of the files/folders are NOT critical at this point.
Basically that's it. If you get Mail up and running, then and only then would I suggest trying to reimport (from MAIL *****) your rss feeds and to do's.
Hope this helps some!