That sounds about right for a thorough scan (although you didn’t state how much data was on the HDD). With archives scanned I would say that was good, but I would have thought it would be more to scan archives as well.

The thorough scan is a much more in depth scan, more so than AVG’s scan, which if I remember didn’t give you any options as to the sensitivity of scan.

I would suggest that you either reduce the sensitivity or don’t start the scan when you are going to be trying to do any heavy work on your system.