Scrubit will clean Badware that hides from discovery by launching off a legitimate program.  This may be the result of a download, or an update by a freeware utility you found on the internet, or possibly from a file sharing program.  Your freeware program has a dependency on the badware in order to run. 

When Scrubit found and removed the badware, your freeware program quit working.  Read the EULA of the freeware program; it may require you to uninstall the freeware program if the badware or adware part is no longer running.  Be aware that some uninstall routines actually try to reinfect your computer with a different threat. 

If you are using Repelit's real time monitoring program, fake uninstall routines are not a problem.  Repelit will auto-clean any illegitimate process from installing anything unknown to you in the background as a result of running a fake uninstall routine.