What is happening is that the repair program is no longer releasing from Safe Mode so some services are prevented from starting, which includes Windows Defender.
Shane produced v4.4.0 which was supposed to resolve this but for some reason it didn't and he is aware of it.
Restore points have been known to revert from this condition but in other cases, a Reset was needed.
There is a Reset option that preserves personal stuff but will delete any programs you may have installed, so if you need to go that route, then you will need the product keys for any paid for programs for when you reinstall them.
I can only apologise on behalf of Shane while he is working for a solution to this bug in his program.