Mail.app needs daily, frequent mailbox rebuilding

When I got my new mbp, I set it up using a Time Machine back up from my old MBP (which never missed a beat).
Now the new machine needs frequent "mailbox rebuild" or it "misses" unread IMAP mail that has been left on the server.
This is quite annoying. Seems like the local cache is corrupt?
Any ideas?

I have a similar problem. One of my IMAP inboxes (default account) is usually empty unless I start up into that folder. Sometimes I can rebuild the messages, other times I have to rebuild then restart the application and not change the selected folder untill its done loading to see my messages.
I have another IMAP account on the same mail servers (and is configured similarly in Mail client) that does not have this problem so I think that makes server side source less likely.
The unread messages number next to the folder name seems to update, but most times, when I try to view the message list, its blank.
I looked for the mail cache as suggested but I dont have any mail cache file/folder there at all.
I tried Thunderbird but had other issues with it. Is there any way to fix my Mail?
Message was edited by: anobjectn

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If someone has a developer account (mine keeps complaining that there is missing information, but there is no missing information and won't let me log in), could you post this as a bug report? I'll deal with my developer account later...
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> It's not that they don't show up in Mail. In Mail, they are in their
(manually) sorted folders. On the server they are in BOTH their
sorted folder, AND the main inbox where they first appeared.
Yes, but what I’m saying is that, according to your reports, even after rebuilding the Inbox of the .Mac account that has the problem, there are still messages in that mailbox on the server that don’t show up in Mail in that same mailbox. Is that correct? This is what doesn’t make sense to me...
> Mac-mydotmacusername1
Mac-mydotmacusername2
[email protected]
So you have two .Mac accounts and a POP account. You hadn’t mentioned this before, had you? I got the impression that you only had one .Mac account...
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<hr>
Try this to determine the scope of the problem:
1. Go to Apple Menu > System Preferences > Accounts and create a new user account for testing purposes.
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Mail.app always wants to have one of my sent emails in the Outbox.
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Thanks Allan.
Good suggestion. Tried it but unfortunately it didn't work. it recreates the Outbox directory in ~/Library/Mail/Mailboxes when I open it. The directory no longer has anything in it (ie no info.plist of Massages folder).
But when I am in Mail.app it still has a message in the outbox. I have to delete it quickly when I open Mail.app, otherwise it will send it.
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I'm using IMAP and my Mail.app at home does not have this problem (both machines are using Leopard 10.5.3)

Mail.app needs daily, frequent mailbox rebuilding

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