When you deleted filelist.txt, you started back over at generation 0. Gen 0 is much larger, and the structures get built much faster, than all subsequent generations (all later gens are 50 structures big).
The score that you receive from each generation is proportional to the square root of the generation number, too, so starting over probably hurt you points-wise. If that matters at all... (it's an incentive to keep people folding until generation 250 -- when the project team has decided they should start over -- rather than starting over when they feel like they need to because of some problem with it getting stuck or producing worse structures).
In short, yes, it's to be expected, you're folding much faster now, but you're getting many fewer points for it.