We have discovered, that Apple VPP licenses for newly purchased applications are not updated correctly from Apple's VPP service.
As of 2016-09-05 6:30 UTC, the licenses are again correctly received from Apple's VPP service. You might have to sync all licenses to get some of the missing apps re-generated. Go to Applications page , Select action Update Apple Volume Purchase Program licenses - Update all licenses selection from wizard.
Please send comments to firstname.lastname@example.org.