The program create a service in order to run some of the repairs as the system account, if that is failing or something is blocking it then it will fail.
Does the event viewer show anything? Also when you open the program are you making sure to only opening it once? Reason why is the program adds the registry keys needed for it to run in safe mode, then removes the keys when you close the program. So if you opened it up twice and closed one of them then the keys where removed and the repairs wont run.
Shane