Lance,
You have caused me to find a structural change in Mail 4.x vs 3.x -- in Mail 3.x, a INBOX.imapmbox folder added a folder within named Attachments, which has some redundancy with respect to attachments. Now it seems that Mail 4.x has added such a folder for POP's INBOX.mbox folder. It does not contain any files from messages received prior to SL and Mail 4.x. I will be testing to learn more about that, but it should not be any factor in this issue.
Where was this Outbox.mbox folder -- is there one also in the Mailboxes folder within the Mail folder, where it properly should be?
The extra files in the one INBOX.mbox are leftover and not needed, and are explained:
http://support.apple.com/kb/TA23076
These leftover files have been known to be problematic in other situations, and might be in this case.
When the new form of mailboxes came into use, conversions of older mailboxes was often incomplete. There is a whole list of comparisons, and things to do to have a more complete conversion, but since you have been using the new versions of Mail 10.4 and/ 10.5 for quite some time, I assume you are not needing to try to find any messages that failed to be converted from when you used 10.3 or earlier, so I have not gone into that.
More later -- I am distracted by a phone call currently.
Ernie