Quick feedback on your post
> >
> <http://[user:pass]@portal.univ.ac.uk/login/index.php>
> 
> > > > ?>postfile:[myc]hts-post0
> > > > This seems to login fine, but only gets files
> > > from
> > > Does the broswer bring up a pop up (http) to
> log
> > in
> > > at that url
> > > or is it a form.
> > It is a form.
> Then DON'T use the HTTP method, use the FORM method
> 
> > <http://[user:pass]@portal.univ.ac.uk/login>
> Use the FORM method

I followed <http://httrack.kauler.com/help/CatchURL_tutorial>
All seemed straightforward, what you see is the result of that.

> 
> > Please excuse my ignorance : near flag ?> get non-html files related
> > Could this be the reason it is not getting
> > .php?ID=xx ?> No, You didn't log in. You didn't filter out the log
> out url. You didn't add the term309 url.

Already picked that up, scan rules read :
-*portal.univ.ac.uk/*
+*term309.portal.univ.ac.uk/*
-*term309.portal.univ.ac.uk/help*
-*term309.portal.univ.ac.uk/login/logout*

Wondering if it is a cookie issue ?