Somewhere along the line my mail app has picked up an extra iCloud account. I think it was when I upgraded to Lion. I suspect the extra account is the cause of some strangeness. The two accounts show up under the Preferences Pane as:
.mac - iCloud IMAP, and
iCloud - iCloud IMAP.
If I select either in an expanded Inbox, I see all of my mail. However, my Junk mailbox only shows junk in my .mac account. The Junk badge shows twice as much mail as is actually there and counts down by 2 as I scroll through the headers.
Any thoughts about if I should (or can) get rid of one of the accounts? I gave up years ago trying to get people to switch from .mac to .me. Too many didn't take the time to update their address books properly or purge their "Recent Recipients" list and I would either get two copies of their messages or just one from the .mac address.