I had this problem as well; couldn't figure out what the issue was for a couple days. After trying out various different things I noticed I couldn't even pull in new Apps onto Blueprints. Lo and behold, I signed out of Apple Configurator, which denoted by Macbook's username instead of the VPP account. I then signed in with the "correct" Apple School Manager account (not the old, original VPP account) and all things started working and flowing without issue.
FIX: make sure you are logged into Apple Configurator with your Apple School Manager account.
