We recently migrated from 5.5 to 2003 exchange server. It sounds like you have to use the AD account cleanup wizard to merge the duplicate accounts. We had to manually add the “self” account to some of our mail clients profile in AD after the migration. Some worked fine and we did not have to add the “self” account at all.
Remember, <b>do not enable or delete the duplicate accounts </b>the cleanup tool will automatically do this for you.