I've had similar experiences, but I think it varied 
from website to website.  I think the problem is the 
website you are downloading always says it has a newer 
version of the file you already have.

From my obsevation of HTTrack during Updates and 
Continue Interrupted Downloads, it appears the HTTrack 
engine re-crawls all the links and asks the server for 
some info about the files (size/date info) without 
downloading the file again.  If the server answers 
with the same size/date info as the local file, 
HTTrack doesn't re-download it.  If the server says 
the file it has is newer, HTTrack downloads it again.  
Maybe the server you want to grab from always 
answers "I've got a newer file" to file requests, thus 
confusing HTTrack.

Have you tried the "Update Hack: limit retransfers" 
checkbox on the Set Options | Spider config page?
HTTrack help explains:

"Update hack 
Attempt to limit transfers by wrapping known bogus 
responses from servers. For example, pages with same 
size will be considered as "up to date", even if the 
timestamp seems different. This can be useful for many 
dynamically generated pages, but this can also cause 
not-updated pages in rare cases. "