Just deleted my .plist for me Apple Mail files and yes, all was well for a while.
I added my other exchange account email and all seemed OK for a while, but after a few minutes, I could no longer see the "sent", "trashed" or "Drafts" files...
Wish Apple Mail was a tad better than "Useless".
Shame, Shame, Shame on Apple for such very, very, very poor software.
p.s. yes I have already sent to feedback
Here's a pertinent article discussing Autodiscovery (feature added for your security in Mountain Lion):
Also when you have mail open, you might try this from Mail's menu: Window > Connection Doctor
It couldn't hurt, and might provide additional information.