That's correct. When you do an individual mailbox backup, Backup Exec connects to each mailbox and backs up the data as if it were a user connecting the mailbox. If the account is disabled you'll also find that the administrator can't access it, so Backup Exec can't either.
Assuming the reason for the account being disabled is that you have a member of staff who has left, it's probably a better idea to simply re-enable it with a new password, which will keep it secure while allowing you to backup the data.
It's annoying I know, but I think it's as much an issue with how MS Exchange works as it is with Backup Exec.
