For some reason, HTTrack is changing relative URLs to absolute after the first
level of the download. It does not appear to be anything with "option value",
"href", or "src" ... the first level seem to be fine, it happens at the next
level of the mirror. I have a lengthy example showing this happening if you
would like to see it. I have tried this in both Windows and Linux, with
version 3.43-9c and 3.33. I get the same results if I ignore robots.txt.

... insert several hours of hacking at the options ...

I think I found out what the issue was ... I see there is an option under
"Experts Only" for rewriting links (internal/external) ... the default is
"Relative URI/Absolute URL" which may explain the change of the URLS from
relative to absolute - except they are all internal links. If I understand
this option correctly, it leaves any internal links (relative paths) as
relative paths and any external URLs as the full URI. On the first level of
the mirror this works fine but on the second level it changes the internal
links to Absolute (external).

I experimented with this setting it to "Original URL/Original URL". This seems
to take care of the relative paths being converted to absolute paths. There
was an issue with it not getting the associated images and lower level html,
but removing version 3.33 and re-installing 3.43-9c seems to have corrected
that. I am going to try and mirror some more sites, I will post more if the
issue persists but meanwhile - if anyone else is getting pages mirrored that
start pointing to the live internet location instead of the mirror, try
setting that option in "Experts only" to Original URL / Original URL.