> I've seen the same problem with a fresh project.
> I think that if I've got this:
> 
> "links scanned A/B (+C)" 
> "Files written: D",
> 
> D should never be bigger than A (or A+C).
> 
> If it were a project update, could D > A(+C) ? 
> why ?
Actually, I'm not sure what I was thinking of when I asked if you were
updating.  I don't know how you're getting those figures :/