Mail is really wonky - some msgs. "gone" after update to 10.4.11

Question

I just updated to 10.4.11, and before I could reboot the computer Mail crashed. On restart of the program (it asked me whether I wanted to use the old settings or new ones, I foolishly clicked on new settings which is where the problem may have begun), I could initially only see messages prior to mid-October of this year. Then Mail began "importing" my entire Inbox, Junk Mail folder and trash folder. I now have 700 messages in the inbox folder (I had 20 prior to the crash), 150 in the trash, and 8 in junk (where despite setting to erase msgs. after 7 days I have msgs. from early December, November and October).
But I still don't have any draft messages visible and my sent mail folder is also seemingly empty, though both are in my library. However, both mbox folders in Mail don't contain any messages, those are in the pop subfolder within mail, and msgs. there have the emlx suffix. And to add to the mystery, the inbox I had prior to the crash is also located within the pop subfolder, not in the main Mail folder. I have no idea where the Mail program is pulling the 700 msgs. in my inbox from.
BTW, have downloaded the emlx to mbox converter and ran the program on my draft messages folder, and now I have a folder on my desktop called Draft Messages containing only one text file.

Answer 1

I just updated to 10.4.11, and before I could reboot the computer Mail crashed.
Are you saying that you kept using the computer normally, and Mail in particular, while the system was being updated, as if nothing was going on? That would have been a really bad idea...
Under some circumstances (e.g. lack of available disk space, filesystem corruption, repeated crashes), Mail may discard the current ~/Library/Preferences/com.apple.mail.plist preferences file and create a new one. This file is where all the account settings are stored. As a result, all the non-.Mac account settings are lost. The messages themselves aren’t gone, and messages stored in custom “On My Mac” mailboxes remain accessible, but any messages stored in account mailboxes become inaccessible until you set up the accounts again.
If you have a .Mac account, that account would appear to have been preserved because Mail would set it up automatically using the System Preferences > .Mac settings. And if you also have .Mac syncing of Mail settings enabled, the other account settings may also be automatically restored that way — which may or may not be a good thing depending on the circumstances, but is definitely confusing if you don’t know what’s going on.
What’s the capacity and space available on the startup disk? Take a look at the comments about disk space in the following article, in case they apply to you:
Problems from insufficient RAM and free hard disk space
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 the filesystem issues, if any, and ensuring that there’s enough space available on the startup disk (a few GB, plus the space needed to make a backup copy of the Mail folder), quit Mail if it’s running, and make a backup copy of the ~/Library/Mail folder (e.g. by dragging it to the Desktop while holding the Option (Alt) key down), just in case something else goes wrong while trying to solve the problem. This folder is where all your mail is stored.
There are at least three ways to restore the account settings other than using .Mac syncing:
(1) Restore ~/Library/Preferences/com.apple.mail.plist from a backup if you have one. Mail shouldn’t be running while you do this.
(2) Set up your mail accounts again (you may want to quit Mail and trash the new com.apple.mail.plist first to start over). If given the option to import existing mailboxes or something like that, don’t. Just enter the account information and Mail will automagically rediscover the data in ~/Library/Mail/ when done. You’ll also have to re-configure some of the Mail > Preferences settings. 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.
(3) Mail may have renamed the old preferences file to com.apple.mail.plist.saved. If that’s the case, you may try trashing the new com.apple.mail.plist and renaming the old com.apple.mail.plist.saved back to com.apple.mail.plist. Again, be sure Mail isn’t running while doing this. Given the circumstances, there exists the possibility that com.apple.mail.plist.saved became corrupt, but that often is not the case and the settings can usually be restored by just renaming the file back to com.apple.mail.plist.
As a side effect of re-creating com.apple.mail.plist, Mail might rename Outbox (which is where messages waiting to be sent are stored) to Delivered. The name of that mailbox is actually a misnomer, as it would contain messages (if any) that couldn’t be delivered for some reason. You can delete that mailbox if you wish.
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It isn’t clear from your post, however, whether there is something else going on and what the situation really is in your case. Some of the things you say don’t make sense to me. Of course the account mailboxes are located within the ~/Library/Mail/POP-username@mailserver/ account folder. That’s where they should be. What makes you think not? Mail wouldn’t recognize any mailboxes at the first level of the ~/Library/Mail/ folder, which is where you appear to be saying you’d expect them to be...
You may want to set up Mail again from scratch and manually import your mail back afterwards as follows:
1. Write down your Mail > Preferences > Accounts settings or take screen shots of them.
2. If you have a .Mac account and .Mac synchronization of Mail data is enabled either in Mail > Preferences > General or in System Preferences > .Mac, disable it before proceeding.
3. Quit Mail.
4. In the Finder, go to ~/Library/. Move (not copy) the entire Mail folder out of there, to the Desktop.
5. In the Finder, go to ~/Library/Preferences/. Locate com.apple.mail.plist and move it to the Desktop.
6. 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.
7. You’ll have to re-configure your Mail > Preferences settings. 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.
8. 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 each of the POP-username@mailserver account folders.
9. If .Mac synchronization of Mail data was enabled at the beginning, enable it again, go to System Preferences > .Mac > Advanced, click Reset Sync Data, and choose the appropriate options to reset the Mail data stored on the .Mac server with the data locally stored on the computer, i.e. sync data must flow from the computer to the .Mac server.
As a result of doing the above, some messages may be duplicated. Andreas Amann’s Mail Scripts has a Remove Duplicates script that you may find useful.
Do with the imported mail whatever you wish. You may move the messages to other mailboxes and get rid of the imported mailboxes afterwards if you want.
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.
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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As to the sent messages date issue you mention in your second post, this is .Mac webmail’s fault. .Mac webmail doesn’t set the Date header on the copy of messages sent that way that it puts in Sent — you can check this yourself by looking at the headers of those messages. If the message’s Date header is missing, then the mail client used to view the message cannot reliably determine the sent date. You’d encounter a similar problem if you used any other IMAP mail client instead of Mail to access your .Mac account.
The problem may not become apparent until you move those messages to a mailbox stored locally on your computer because messages on an IMAP server have an Internal Date attribute independent of the Date header. Unlike the Date header, however, the IMAP Internal Date attribute isn’t part of the message, and hence, is lost if the message is moved out of the server to a locally stored mailbox. I believe Mail uses the creation date of the .emlx file associated with the message in those cases — and that timestamp changes every time you rebuild the mailbox or re-create the index...