Ask the Library: Reference

You probably have a section break where the separation of the documents is happening.  There isn't anything you can do through the print options, you need to merge the two documents into a single document.

If you don't have access to the full version of Adobe Acrobat you can find sites online that will merge PDFs into a single document.

If this is your master's thesis you can contact Michael Pujals in the Library and he can help you out too.