In the box below the HTML Inserts:Header there is a line of text that appears (<a name="Top"></a>)
where the default comment says this should be blank. This shows up as an error in the W3C Validation.
I removed it from a test site and there was no issue with it so I am assuming that this is a typo that relates to the latest version update. I am using Atahualpa 3.7.3

That has never shown in any of my 3.7.3 installs.

It was in both of the sites that I updated to the latest version, but on checking a third site that is still on version 3.7.1 the text also shows up there!
Not sure where this is all coming from?

It looks like it is code so you can click a link at the bottom of a page to return to the top via anchor tags.

That what I thought, but on the older version of Ata we are not using that kind of feature.

I don't know what to tell you. It is not a part of Atahualpa.