I do have SuperDuper on my desktop as my external hard drive.Do you mean that you have a cloned external drive? If that's so, launch SD and click Schedule to see if SD is trying to update your clone during the time in question. Reset if necessary. If that fails, I would contact the developer for advice. I couldn't find a SD preference file in the usual location but I did find a SD folder in ~/Library/Application Support. I don't want to tell you to play with anything in there so it would be best to go to
the Shirt Pocket site and click Support to send an email.