Its OK I fixed it. It is nothing to do with HTTrack.  I will post the fix in
case anyone has similar issues.

It was a badly coded website using CSS in files with the same name as the html
file but with number appended and then some arguements....wierd!

<link rel="stylesheet" type="text/css"
href="index1a1.html?startcss=true&amp;ts=1390316678" />

I renamed the file index1a1.css and removed the arguements and it works:
<link rel="stylesheet" type="text/css" href="index1a1.css" />

It was a site-builder website, I guess they use some weird and badly coded
solutions!