Hi,

I understand that when you send out email from your msn account the recipient is seeing an Hotmail.com email address, it is because of the Alias that you might have added for the msn.com email address.

Alias Email addresses are alternate addresses that deliver messages to the same mailbox.  They allow you to hide your "real" msn address.  You still log into Hotmail with your MSN Live ID and when you send emails through your msn account the recipients see the emails,  that appear to come from the alias address, but you're still using your same Windows Live ID.

In order to resolve the problem you need to delete an alias, please refer to the steps below: 

Deleting alias

1.Go to https://account.live.com/

2.Click Notifications then Manage email preferences 

3.Under Other email address, click Remove on the email address and follow the remaining steps.

If the issue still persists, please check the private message below

Thanks and Regards,

Mubarak