"IMHO you'll always come across performance bumps when using network drives. How can you tell for sure that non-perl programs don't have that problem? Are they accessing those 60,000 files as well? "
Yes, in fact they run over the exact same 60,000 files. There is a slight performance bump of ~30 seconds, from 13m14s to 13m35s. Compare this to a 2+ hour increase.