First every mail sent shows up in the draft folder even after it was sent, now sent messages show as unread, anyone else seeing this? Weird behavior since Snow Leopard.
Probably the result of some issue with indexing, particularly the Unread tag. You may want to use Rebuild on the sent mailbox of this account. If so, be aware that during Rebuild all message briefly disappear, so don't panic, but patiently wait for Rebuild to finish.
I just rebuilt all of my mailboxes (hours long overnight) to try to correct the unread email count in “smart mailboxes”. That didn’t work (it is still counting double) but it did give me the added bonus of sent email being saved as drafts (not deleted when sent) and marking newly sent email as UNread.
I was having similar problems with one of my IMAP accounts in Mail where it was showing unread emails though I had read them on my iPhone (hours & days before). I searched around a bit and started suspecting a couple of plugins I had demoed but was no longer using. I thought they might have been causing problems so I removed them as follows:
I quit Mail, went to MyHomeFolder>Library>Mail>Bundles and deleted the .mailbundle files. Different plugins install differently as I found, so you might also check for files in Macintosh HD>Library>Mail>Bundles.
Depending on what plugin you are using, and if the demo has expired, you might even find a "Bundles (Disabled)" folder with .mailbundle files.
After deleting the .mailbundle files, syncing with my IMAP began to work normally.
I didn't do extensive testing, I just go rid of all the .mailbundle files, so I don't know which plugin was causing the problem, I also no idea if this will help your issue, but you might look into it if your are still experiencing the problem.