When a user logs into the helpdesk app using Windows authentication for the first time, the system connects to your Active Directory and tries to get the user's information from the AD. Including his email address.
If a user-account with this email is ALREADY present in the helpdesk system, it means the user had already sent some emails into the helpdesk, without logging in. The system understands that - and instead of creating a new user account in helpdesk-database - it uses the existing account (by updating the username and other info). To preserve the ticket history and all.