I think this probably has to do with your settings in Settings>Main>Included folders and Settings>Excluded>Folders. Can you send me what those are?
Also, no issues reinstalling the app. You do not have to pay for it again.
Also, consider contacting us at support@fstopapp.com. It is a little easier to help you. I or you can post the solution here (once we find out what is wrong) so others can benefit.
