Hi

I had a simmilar problem with a site having files unter direktorys acessible
trough the direktory listing, but not linked from the html files.

foo.com/bar/stuff.html <- some files linked like narf.txt
foo.com/bar/ <- other not-linked files like zoit.zip

I did it this was:
Dowload the Site, then use (under linux) "tree -dfi > linklist.txt" to get a
listing of all the subdirektory path. Clean it up in an editor (removing the
./ infront of the lines) and load it into HTTrack again as a source link list.
This way he explicitly trys the direktorys by listing them.
Repeat these if necessary for deeper directorys.

Hope this helps...