I have just this second realised that the page I am getting from the protected
area is the page that is displayed for a split second after I click the "log
in" button to get to the protected content in the first place.

Therefore, I am guessing HTTrack is simply pulling the data to quickly and
doesn't recognise the 'redirect' or whatever is actually happening.  I have
looked through the settings and can not see what this might be?  Perhaps
something in the "Experts Only" tab, and you have probably guessed by now I
fall well short of expert :(