> WinHTTrack Website Copier 3.31-TEST-2 (+swf)
> I found that pages with 
> <META NAME='robots' CONTENT='noindex,nofollow'>
> (and only these ones within the mirror)
> had their relative links transformed into absolute links.

You mean http:// links ?
> Is there a reason for this behaviour ?
Yes - if robots.txt are enabled, "nofollow" in meta will 
force httrack to skip ALL links in the page.

(Err, isn't it the desired behaviour ?)