Did some more testing, it seems all my uploads, which I added through the bulk importer, do not have any page template set. When I set one of the to any template and THEN ran the default values updater it did switch the template. This seems to be an issue with the bulk uploader not assigning a template. Is there a way I can get this default values to recognize this? I could even do a SQL query or something if you let me know where this info is located.
This might also be something for you to consider if you want both of these plugins to play nicely.