>  BUT! if I keep trying all the links, they will 
eventually 
> work (while offline), then not
> work a minute later, then work again.

Maybe a glitch due to the browser cache ?
Anyway this problem can be caused either by missing scan 
rules (files weren't caught - in this case define 
additional filters in 'set options'/'scan rules'), or 
by "evil" javascript inside the pages (which httrack could 
not detect - nothing to do here unfortunately)