You might want to watch it when it first starts to see if it starts over and over again. If necessary temporarily disable those as well. Running Scandisk first is also a good idea. Scandisk can also be interrupted by the above. Even though you shut everything down in the Close Program window there is still other stuff running.
Safe mode is the way to do it.
You can remove the AutoUpdate notification by clicking the Update Reminder icon and then either installing the recommended updates or clicking Remind Me Later. If you see this icon, double-click it, pull down the Index menu, and choose Pause Indexing. Close Find Fast and close Control Panel. The things that are being bypassed are the startup programs that cause the restarts in defrag and scandisk. If the number of files checked continues to grow without restarting then it is working properly.