You stated you resume the mirror.  On the second page, the one with the Set
Options button, the Action has Update Existing Download and Continue download. 
Are you using continue?
Under options -> Spider -> Update hack (limit re-transfers=checked)

Finally I stated that 3.41-2 has multiple problems in
<http://forum.httrack.com/readmsg/15842>

3.32 works fine, it will check the files to see if they are different than
what it already has and only download what has changed.