Wheter it works perfectly on serv-u is irrelevant, as it's based on different API calls. Overlapped IO (usinc completion ports) is much harder to manage on driver level, and improper implementation could result to what you've experienced.
Driver in this case can be;
1) harddrive controller's driver
2) network adapter's driver
3) 3rd party driver hook (virus scanner, firewall, ...)
I'm not sure, if there's any way to debug this... also 50% cpu usage sounds high for such speed (if it's average; on 2ghz p4 it should be closer to 0 than 50
- ofcourse external scripts may have effect on this, as they add overhead)