> If I break a download with ctrl-c, I(nterrupt), then 
later 
> do a httrack --continue, it deletes everything and 
> downloads it again. Luckily it's cached in the proxy 
> server, but it's a little worrying. 

Weird.. first ensure that you are using a recent (3.2X) 
version.

Also ensure that you don't have directory problems ; that 
is, use something like:
httrack --continue -O .