I am surprised they ever ran in safe mode lol
The reason why is in order to run a repair as the system account my program makes a service and then runs the repair from there. This is how it has always done it. Well in safe mode only the allowed services set in the registry are allowed to run. If you went and try to start another service it wont let you.
So because of that it shouldn't have ever worked in safe mode. Thats why I ask people to do a clean boot instead of running from safe mode.
But at the same time, in the last few versions I now have the repair try to run as the trusted installer service, only the file permissions repair. That also installs a service and runs. If it cant find the trustedinstaller.exe running then it will run the repair as the system account.
Shane