More information on this:  In the hts-log.txt I found that for *every* file
that eventually gets overwritten, there is an Info message listed similar to
this:

10:24:43	Info: 	engine: warning: entry cleaned up, but no trace on heap:
intranet/js/web.js (C:/Documents and
Settings/Username/Desktop/HTTrack/Website/intranet/js/web.js)

Then a little while later...

10:26:28	Warning: 	Unexpected 412/416 error (Requested Range Not Satisfiable)
for intranet/js/web.js

Might this be a bug in HTTrack?