The account which is used to run ExMerge utility must have "Send As" and "Receive As" permissions on the corresponding Mailbox store. The built-in administrator accounts as well as the built-in administrative groups inherit the Deny permission for both the "Send As" and "Receive As" permission. As a result Deny overrides the Allow permission which you can set manually through ESM. A clean and functional approach is to create an account for ExMerge with the necessary permissions.
Note: Screencast, How to ExMerge Mailboxes in Exchange 5.5 Server, is available here