email@example.com. firstname.lastname@example.org and email@example.com are all the same thing: emails to all three go to the same inbox. You must presumably have gone through the migration process from MobileMe to iCloud before 1 August last, or you would have lost access to the account. However if you didn't set up Mail for the different iCloud server settings I wouldn't have expected to go on working this long.
In any case, I would suggest you delete the account from Mail (this won't delete anything on the server) and set it up again from scratch following the process described in this illustrated article: