Okay, so I went back to an original build site backup and cloned that and tested. I did this process twice from the same backup.
One time I just left GP Premium v1.0 active (v1.1 update was visible) and create a clone.
The other time I disabled the licence, plugin and theme. (v1.1 update was visible prior to disabling). I then created a clone of that.
I installed both clones on the same directory at different times and both installs would not provide me access to the GP Premium v1.1 update.
Everything else site wide seems fine.
I don’t get it. Any more suggestions?