It might be you have an Anti Virus program or tool with an option activated causing it to monitor/viruschecks in realtime all file accesses/reads/writes. That slows down things a lot.
Or a tool that maintains some database.
A tool called FileMon (google for it) which is similiar to SnoopDos on the Amiga might give some hints.
I once had a rootkit virus which also caused massive slowdown.
