I am also having issues with my work exchange serve and Mountain Lion's Mail application.
After reading this and another thread, I found that if I open Mail's preferences and go to the Accounts pane, my "Internal Server" has indeed been set to "sites" by some bug in Mail. If I set it back to the actual name of my internal exchange server, mail begins coming in properly. Everything seems to work ok.
As others have noted, though, if I close Mail and reopen, the Internal Server gets set back to "sites" andI have to reset it, CLOSE the program, then reopen.
So, change, save, close, reopen = Mail starts working. THEN close and reopen one more time, and Mail STOPS working (because it gets reset to "sites").
(I also deleted all references to my mail exchange server in my keychain using the /Applications/Utilities/Keychain Access tool. Not sure if that was necessary or helpful.)