Did most recent Audio update to OSX and Mail.app went insane.

Question

I switched to the Mac in... November? and have absolutely loved it. This has been my first catastrophic experience thus far and I'm used to Windows being a part time job to manage so I'm not complaining.
However, late last week OSX installed an audio update of some sort and when I rebooted mail.app had seemingly lost it's mind:
1. IMAP accounts constantly go offline and then back online at random time intervals. This problem I actually had occasionally before but now it's a constant annoyance.
2. Frequently getting "The message from "somebody" concerning "something" has not been downloaded from the server. You need to take this account online in order to download it." error message for messages that have a. already been downloaded and b. who's accounts are showing as online. FYI, yes I do have mail.app set to download and keep a copy of the messages locally.
3. Some messages (I can't find a pattern but it's about 5% of the messages) download repeatedly and appear in the inbox as many as 51 times. The only solution to this seems to be to log into the IMAP account's webmail access and delete the "offending" message.
4. An account can be online and yet not show all the messages that are in the inbox. I know this because if I log into the webmail I can see them.
5. Seemingly randomly the rules are ignored. Typically I can select a message and then tell mail to apply rules and then it works but why didn't the rule happen on it's own as usual.
6. The general "Inbox" sometimes doesn't show new items in the individual account inboxes until I go and click on those individual account inboxes and then come back to the general inbox.
Info about my system/setup:
a. I have 4 IMAP accounts.
b. I store messages on the IMAP server.
c. The "fullest" IMAP account has roughly 500 MB in it but is set to have 2.4 GB capacity on the IMAP server. That account also has 48 personal folders on it, and has had them for a little over a month. After reading about smart folders, I intend to consolidate many of these into an "Archives" folder.
d. The other IMAP accounts are each set to have 1+ GB of available server storage but each have under 100 MB used.
e. I use SpamSieve for email (love it, by the way)
f. I have a demo of MailTags running (it's been since mid-June and I've only played around with tagging a few emails so far but I intend to use iGTD once I get Mail back under control)
What I've tried:
1. I read that it's better to do the consolidated updates than the incremental ones so three times now I've tried to download the consolidated OSC 10.4.10 update but it never fully downloads. I'm not sure what's the deal with that as I've downloaded 300-400MB files over my internet connection at other times without difficulty.
2. I read that you can delete the folders in mail.app and let it rebuild them from the IMAP folder... a. from what I read, I'm not clear on the procedure for doing this safely b. I have a lot of folders to deal with and c. the only places I've read about it is from people commenting in forums that it didn't help them.
So... any suggestions?

Answer 1

At least one of the problems you have appears to be some index corruption, and I have the feeling that MailTags has a bearing on it. I don’t think you’ll be able to completely solve the problems you have without uninstalling that first...
Go to Apple Menu > System Preferences > Network, choose Network Port Configurations from the Show popup menu, and make sure that the configuration used to connect to Internet appears at the top of the list. Leave checked (enabled) only the port configuration needed to connect to Internet and Built-in Ethernet (in that order if not the same), uncheck (disable) the rest of network port configurations and see whether that helps — if it doesn’t, turn ON again the ones you want enabled.
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), try this:
1. Quit Mail if it’s running.
2. In the Finder, go to ~/Library/Mail/. Make a backup copy of this folder, just in case something goes wrong, e.g. by dragging it to the Desktop while holding the Option (Alt) key down. This is where all your mail is locally stored.
3. Locate Envelope Index and move it to the Trash. If you see any other “Envelope Index”-named file there, delete it as well.
4. Move any “IMAP-”, “Mac-”, or “Exchange-” account folders to the Trash. Note that you can do this with IMAP-type accounts because they store mail on the server and Mail can easily re-create them. DON’T trash any “POP-” account folders, as that would cause all the mail stored there to be lost.
5. Open Mail. It will tell you that your mail needs to be “imported”. Click Continue and Mail will proceed to re-create Envelope Index — Mail says it’s “importing”, but it just re-creates the index if the mailboxes are already in Mail 2.x format.
6. As a side effect of having removed the IMAP account folders, those accounts may be in an “offline” state now. Do Mailbox > Go Online to bring them back online.
Given the amount of mail you have on the server, I expect it to take a fair amount of time for Mail to fully re-create the index and bring all the mailboxes back online. Again, I strongly encourage you to uninstall MailTags before doing that.
Note: For those not familiarized with the ~/ notation, it refers to the user’s home folder. That is, ~/Library is the Library folder within the user’s home folder, i.e. /Users/username/Library.