Are you running Esri License Manager 10.4 also? This is a requirement for Pro 1.2 licensing.
If licensing through Portal for ArcGIS, which is approximately a private version of ArcGIS Online, installation of Portal for ArcGIS 10.3 or later and ArcGIS License Manager 10.4 is required.
I also have Portal 1.3.1 and made the upgrade to Esri License Manager 10.4 , but
I still got the warning "Not all requested extensions are available." Do you have some