> At the root of my site I have a file 'index.xhtml' and I'm
> out of luck since HTTrack stop there and don't follow any 
link.

Can you check this file's type please ?
In hts-cache, open the new.txt file, and find the 
corresponding line (probably the first or the second one), 
like:

16:15:32	9405/9405	U-----	200	untouched 
('OK')	text/html	etag:%22fc41-24bd-465ab500%22
	linux/~roche/1.html	D:/My%20Web%20Sites/xx%
20let/linux/_roche/1.html	(from )

The type is written on the 7th column (here, text/html).