This could be caused by the "Notes", specifically when the master template have no notes inside the slides and the knowledge source content have notes for certain slides.
This issue is Office 2013 specific.
To resolve this issue all that needs to be done, is for notes to be added to the PowerPoint slide which does not have notes. It does not matter what the notes say, just as long as PowerPoint registers the notes exist. After adding the note in the PowerPoint presentation (master template or Knowledge Source content) save the Slide and Approve if need be. Then test.