It can either be run as administrator or you can change ownership of the files and subfolders (this is what I did).
This solved the issue, however, frankly I was quite annoyed that a program was insistent that I update it only to have a newer version that had issues with file permissions and where the installer didn't put files in the USER folder that needed user permissions. I understand things have to be pointed to properly to ensure it works, however, seeing that this time wasn't taken is disappointing.
Also, I think installing it in a different folder to get around permissions and defeat the OS's directory structure (it's the way it is for a reason) is stupid.
