Missing messages and other recent Mail.app quirks

HI,
Although I've read through many post on this issue, I haven't found one that seems to apply to my situation. And, the process seems really confusing... so I thought I'd ask you guy's.
I rebuilt my inbox's last night, and:
1. 1 of my 2 POP inbox's is now empty (except for a couple new mails today). There were about 150 messages.
2. My .mac inbox is receiving mails, but first the little spinner thing wouldn't stop spinning, and has switched to a blue clock looking thing that's stuck at about 10:30 (may have moved to 11:00 now?).
3. Drafts don't seem to be saving.
4. Seems that the audio feedback is gone or was gone (the sound is up and the speakers to work).
5. I was getting a strange error message when sending that I didn't write down (something to do with the Trash and 0 space or something).
I've been on this new machine (OS 10.4.5) since November with no Mail.app (2.0.7) trouble at all (I moved from a TiBook that had once had Panther on it). And, I didn't let this last Security update install. I had been trying to resolve some POP SMTP server issues, but went with .mac with the "reply to" option (I'm stuck in a hotel in southern China), and I did lose one email that I had just sent... which prompted the rebuild of the mailbox's. Still can't find that missing email- but I did get a reply from the person I sent it to.
There weren't many messages in that now empty inbox, but they were the important ones (which I think I located in Library > Mail folder thanks to you folks).
I can survive with issues 2 - 5 above if necessary, but I'd really like to deal with the missing message problem.
Should I just "import mailbox's" back in and hope it all works? Will I lose those new mails from today? Can you offer me any advice?
Sorry if I rambled on too much (too much spare time on a Sunday morning in China), and thank you in advance for any thoughts,
Guy

Guy,
Different answers for each file. The CachedData1 is a leftover file from an IMAP or .mac account -- Mail no longer uses that method of caching, so delete.
The two MessageUidsAlreadyDownloaded are used with each POP account, and are still valid file types -- however, one of them should be modified each time you access your POP server -- check the dates modified again.
The two files named to begin with Incoming are leftovers, and probably must simply be deleted. They resulted in the mailbox where you found them when a message had been received (even if by transfer) and that mailbox was not opened prior to the conversion. In Panther, and earlier, these files would disappear when the mailbox was opened to view. It probably is only one or two messages -- the Incoming_Mail file can be read with TextEdit to confirm.
I think the Envelope Index Journal results during an incomplete indexing attempt Mail has made at some point, was meant to be temporary -- I am not entirely sure about this, but I do not have one.
The time out on port zero is one I need to research -- although I have seen a few reports, and think there is some explanation, I cannot remember as I write this.
There is an ongoing issue with .mac and continuation of the indicator for activity -- I see this on my iBook G4, but not on my G5. Useless needed for Offline use, set Mail Preferences/Accounts/Advanced to Don't save all message and attachment for Offline viewing, which may help. I hope this one get addressed in some future update.
Ernie

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