It sounds like httrack just doesn't work properly for large websites if you
restart it.

The only suggestion I have left is to leave your computer on and do it in one
go.

If that's not possible, then you might be able to run it in a virtual machine
(because the virtual machine would think it's still turned on when it's
paused). But those are just guesses; I've never tried the virtual machine
approach.

At this point I would hope that one of the experts like Xavier Roche or
William Roeder can step in with some advice. They used to post here a lot. If
you mail them you might get their attention.

Sorry for my own late reply. I was just trying to help people out in my spare
time but school got busy again so I don't have much spare time left (until
2015 maybe :-))!