> When I look at the mirror I find 2 copies of every file, 
1 
> with the correct name (e.g. index.html) and one with a 
> something extra (index-2.html).

It happends when you have two references to the "same "file:

<http://www.example.com/>
and
<http://www.example.com/index.html>

HTTrack can not safely "guess" that these files are 
identical, and hence create an additional -2 file.