Mail problems won't go away! Help!!!

At first, I tried dragging messages that were marked "not junk" from the junk folder to the inbox. It used to work. But then, they would disappear. Then I noticed that all of my sent messages were marked as junk. Now, I keep losing sent messages. I'll click on the sent messages folder and I'll see messages that I just sent dissappear. They are there for a half second and they're gone. I often don't know if the messages were sent. The drafts folder will sometimes keep messages even though they were sent. Or messages will reappear mysteriously in the drafts folder.
I tried the routine of trashing certain files/folders in the mail/library/home folder. That never worked. I tried getting rid of a lot of messages in my inbox and sent messages. I was at about 3000 in my inbox and I'm down to less than 600. Then I tried the trashing certain files/folders in the mail/library/home folder again. It didn't help. I called apple support. They could not solve the issue but recommended an archive & install. I tried that a few times. It seemed to help for a day or two then it was back to being weird. I then tried trashing all files and folders having to do with mail in the home library and system library folders and doing another archive & install. Again, it helped for a couple of days but the troubles have returned. The are still some files somewhere that keep track of my .mac info. Because even when I trashed everything I could find having to do with mail, and did an archive & install, the mac still remembers my .mac account and the email addresses that I have written to in the past. So, maybe those files, whoever they are, are causing the problems.
Powerbook G4 Mac OS X (10.4.8)

Your problems are caused by data corruption within your home folder. Reinstalling Mac OS X preserving your data obviously cannot fix that. And if you have a .Mac account and have .Mac synchronization of Mail settings enabled either in Mail > Preferences > General or in System Preferences > .Mac, getting rid of the potentially corrupt files won’t work either because Mail will restore them using the (corrupt) synchronization data stored on the server.
Verify/repair the startup disk (not just permissions), as described here:
The Repair functions of Disk Utility: what's it all about?
After having fixed all filesystem issues, if any, proceed as follows:
0. Quit Mail if it’s running.
1. Go to System Preferences > .Mac, disable .Mac synchronization of Mail settings, and reset the synchronization data currently on the server.
2. In the Finder, go to ~/Library/. Move (not copy) the entire Mail folder out of there, to the Desktop.
3. In the Finder, go to ~/Library/Preferences/. Locate com.apple.mail.plist and move it to the Desktop.
4. Open Mail and set it up again from scratch. If given the option to import existing mailboxes or something like that, don’t. Just enter the account information and check that everything works fine.
You’ll have to re-configure all your settings in Mail > Preferences. For spam-related security reasons, the first thing you should do is go to Preferences > Viewing and disable Display remote images in HTML messages if it’s enabled.
5. If Mail works fine now, and you had any messages stored in local mailboxes, do File > Import Mailboxes, choose Mail for Mac OS X as the data format, and follow the instructions to import your mail from the old Mail folder that’s now on the Desktop. Import the Mailboxes folder first, then the POP-username@mailserver account folders, if any.
As a result of doing the above, some messages may be duplicated now. Andreas Amann’s Mail Scripts has a Remove Duplicates script that may help to fix that.
Do with the imported mail whatever you wish. You may move the messages anywhere you wish and get rid of the imported mailboxes afterwards.
If all is well and you don’t miss anything, the files on the Desktop can be deleted, although you may want to keep them for a while, just in case.
Ask for any clarifications or if you need further assistance.
Note: For those not familiarized with the ~/ notation, it refers to the user’s home folder. You can easily locate any of the folders referred to in this post by copying the folder path here, doing Go > Go to Folder in the Finder, and pasting the folder path there.

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