Mail.app shows my .mac inbox is empty. all other tools show it is not.

Question

a few days ago mail started acting strangely on my .mac account. it would indicate that i had a large number of unread messages in my .mac inbox, then when i looked at the inbox in mail, it would show up as empty.
i started to think that there must be some kind of problem, so i quit mail and checked via webmail. webmail can see all the msgs in my inbox. i quit and try mail.app again. same result (mail shows 0 messages).
i try forcing a "synchronize" from within mail (from the mailboxes menu). there is no change. i try a "rebuild" command from the mailbox menu. there is no change.
i try firing up entourage and it sees the mail in my inbox. i quit entourage and try mail again. no change (mail shows 0 messages).
i suspect that there is some kind of corruption or something either in the local state on my machine or perhaps a message which has some malformed headers or something which is sitting in my inbox and causing mail.app to be unable to properly download the mailbox contents.
i tried using webmail to go in and either delete the messages or move them aside to a separate temporary mailbox. back in mail.app, it sees the new temporary mailbox and at first indicates that it has ~40 or so unread msgs (which is true plus about 10 more read msgs), but when i actually click on the mailbox to look at it, it appears empty. i reconfirmed that webmail and entourage can both see ~50 msgs in the temp mailbox, but mail.app shows zero.
also, in addition, the same problem still holds for my inbox. so now when i send myself a test message, mail.app temporarily indicates that i have new mail, but then when i look in my inbox, nothing appears in mail.app. if i quit and go look at my inbox with webmail or entourage, i can see the new mail as expected.
i looked in system.log, console.log, and mail.log and didn't see any log msgs that seemed to relate to whatever problem mail was having reading the headers/contents from the server.
so i was trying to fix the problem by clearing out my inbox using webmail, but instead it appears that i have merely replicated the cause of the problem so that it now affects two folders instead of just one.
does anyone know of a way to definitively clear out a mailbox altogether on the server? it would be reassuring to know that there was not some hidden corrupt msg sitting in my inbox messing things up.
any other suggestions for how to get out of this state? thanks.
  Mac OS X (10.4.5)  

Answer 1

oh forgot to mention a couple other clear signs that mail.app is "confused" here:
if i right click on a mailbox in the mailboxes window and select "get info..." (a very useful command hidden in an odd place), it shows me that right now my inbox has 3 messages and my temp mailbox has 50 messages. but when i look at either of these mailboxes normally, they show up with zero messages.
if i send myself a test message and then tell mail.app to check for mail, the new message indicator comes on and my inbox temporarily shows up as having 3 new messages. then when i click on it, it shows up as empty and the new message indicator goes away again. if i repeat this it will say 4 new messages, etc.
so it's acting like there's some kind of corrupt partial message at the top of my inbox that mail.app can't read and keeps choking on. i've had this happen before on other imap servers a while back. for those servers, i had normal login access, so i could go and edit or delete the offending file. in this case (apple's .mac server), i don't know how to do the equivalent.