The chances are that unless you are actually running windows no external HD is 'seen.'
The reason for running scandisk in DOS is usually because of interminal delays and restarts which can happen while running from Windows. I think that if you select only the External HD when doing that, there won't be any silly result.
My reason for DOS was, as you say, to avoid delays and restarts. However, I rather like the disc "map" that DOS displays.
In the Maxtor manual, it states that Scandisk can only be used with W98SE on partitions of <127GB. I am uncertain what is meant by "partitions" but, as my HD is 120GB, may I assume I can use Scandisk within Windows to check my new HD?