It isn't really a problem, so to speak, as everything you describe is normal. Your scanner software, and scanner, are "pinging" the computer, to make sure that you have a connection; everytime this happens, you interrupt the Scandisk, and it makes it start over.
So, you know what you have to do.
Also: You could boot into safe-mode, and run scandisk, but that is more of a pain that just unplugging the scanner.