I started having the same issue after the upgrade to 11D. Come to find out, in the job setup, expand your Exchange server, Microsoft Information Store. Simply check the First Storage Group box. You'll notice that you don't have option of individual mailboxes (you do if you choose the MS Mailboxes, but that is where you are getting the error from), this is using the Granular Restore Technology and it backs up Exchange a lot faster than the old days. In the old days, Backup Exec would have to log into a mailbox, back it up, then log out of it. If you have a lot of mailboxes, this could take all night. Our Exchange BU use to take around 10 hours and now only takes about an hour.
Granted it seems to take a little longer to restore an email to someone's mailbox, but that happens rarely and I do enjoy coming to work in the morning and seeing the BU job has completed sucessfully. 776Gb in 11 hours.