Mail sick after Leopard upgrade

Question

Hi everyone
I originally added my comments to another thread, but that person's problem has been solved, while mine has not, so I had better post separately.
I had no problems with Mail before I upgraded to Leopard. After I upgraded, Mail wouldn't boot. That turned out to be due to an older copy of Mail still being on my disk, and the Dock and Login Items calling it instead. Deleting the old copy and opening the new copy, so it could run its Leopard setup, fixed that problem. After that, Mail would boot.
However, I was unable to download any mail from my POP server. It worked fine before the upgrade, but wouldn't work after the upgrade. Similar to the other thread, the Activity window would say that messages were being downloaded (and SpamSieve would log them), but they would not appear in my Inbox. Strangely, mailing-list messages etc. filtered to other mailboxes would appear in those other mailboxes.
I have quite a few extra mailboxes. The Leopard upgrade has rearranged them. They used to be listed under the Inbox and Smart Mailboxes (I installed MailTags once, but had problems with it, so I uninstalled it, but the Smart Mailboxes I created remain). The whole hierarchy, from the top of the sidebar, was called "On My Mac".
After the Leopard upgrade, "On My Mac" no longer represents all my mailboxes. It has been shifted down the sidebar, and now only contains my extra mailboxes (mailing lists etc.). My Inbox, Sent, Trash, Junk and Smart Mailboxes are now separate categories to On My Mac, and listed above it. I have no idea if this is relevant or not, but I mention it in case.
Following a suggestion on this forum, I tried rebuilding my Inbox. Mail crashed. It crashes every time I try to Rebuild my Inbox. (Crash log: http://www.riverland.net.au/~clytie/Mail_rebuild.txt).
After my attempted Rebuild, my Inbox was empty. All my previous messages had disappeared. There are plenty of emix files in my ~/Library/Mail POP account folder, but oddly, they are very old, many from previous years. Yet I only keep a couple of months' emails in my Inbox! None of these recent mails remain.
I have turned off Time Machine, so I won't overwrite my previous backup. (I don't know enough about Time Machine's bevaviour yet to take any chances.) My previous backup shows emix files up to the day I upgraded to Leopard, but double-clicking on them only shows a title and an empty window. (This may be because they are on a separate disk to the Mail app.: I don't know.)
I noticed that the Activity window would get stuck downloading specific mails, so I got onto my ISP's Webmail, and deleted as many mails as I could (some mailing list mails, spam etc.). Rebooting Mail after that, I could download a few mails, but again the Activity window would show Mail stuck on another message (usually in the 50s or 60s: "downloading 52 of 694"). If I delete that message in my Webmail, Mail will get stuck on another message next time I Check Mail. (I tell the Activity window to Stop, and it says it is Stopping, but never finishes. I have to Force Quit to stop it. Is mdworker related to Mail?)
I don't know if these "blocking" messages have anything particular in common. My prefs on my MacBook or my ISP don't exclude messages on the basis of size, format or attachments.
I use SpamSieve, GrowlMail and PGPMail. SpamSieve appears to be working: it logs each message received, even though they don't appear in my Inbox. However, SpamSieve's Growl notifications don't appear. I am unsure if Growl is working with Mail, although it still shows up in the Mail prefs: it is working with Speed Download. PGPMail still shows up in the Prefs and menus, but not in the message windows.
I hope this information is useful. I don't know what to do from here. Thankyou for any help you can offer.

Answer 1

My question hasn't been answered here, but I seem to have found the answer myself, eventually.
I decided to move the GrowlMail and PGPMail mailbundles to the Bundles Disabled folder, plus delete my two remaining MailTags smart mailboxes from when I had MailTags installed, then restart.
Lo and behold, as my old Grannie always said, I could successfully rebuild my Inbox. All my much-regretted previous emails appeared again! It was an emotional reunion.
Then I tried checking mail, and LaB again, several days of mail came pouring in.
Evidently something to do with the mailbundles or old smart mailboxes was getting in the way of Mail function.
I'll try reintroducing each mailbundle. I hope nobody else has this problem, but just in case, I thought I'd better leave my belated solution.