I've seen this problem partially described in many posts but none of the solutions work. When I try transferring files from a Windows 2000 Server to a Windows 2000 Professional Workstation, the transfer rate is unbelievably slow. To copy a 300 MB directory takes anywhere from 331 minutes to 111 minutes when it should take less than one minute. This is a 100MB Cisco Switched network, all ports configured to 100MB Full Duplex. Both workstation and server have SP1+SP2 installed. The server is a Compaq ProLiant M370 running at 933Mhz w/ 1GB memory. The drives are RAID 5 configured. This server is also the Domain Controller running DNS, which seems to be correctly configured with the exception that the Active Directory Users and Computers MMC takes an exceptionally long amount of time to initialize (to be saved for another post). The Workstation is a Dell OptiPlex GX110 with 192MB memory and 3com 905C 100 NIC. I have already deleted the Scheduled Tasks from the workstation registry to no effect. This seems to be more related to collisions and/or TCPWindowSize as changing the values suggested in http://support.microsoft.com/directory/article.asp?ID=KB;EN-US;Q169789 seem to help but not significantly to fix this problem. Unless the values need to be changed on the server as well, which I have done nothing to other than disable the virus scanner (also no effect). On another note, this problem exists on maybe 85% of my W2k workstations, but not all of them, even though they are installed the exact same way.

With the compatiablity of these two systems it does not seem as though it should have this type of problem..Wow I hope someone answers this for you because I am bafled.

Wow, BIG post.

But anyways... you might try setting up two test systems that are the same. Take one of the W2K systems that transfers fast and one of the ones that's slow (hopefully the same model). Then transfer the same size file and time it to double-check. Next, switch their physical network ports around to make sure it's not the physical wiring (cross talk, bad cable, etc).
So then you've narrowed it down to the server end of things or the machine end of things and not all the junk inbetween. Next, check your NIC settings against each other, maybe try manually setting them instead of using the default auto negotiate.
And double check your protocols to make sure you're only running TCP/IP. Might also try running a TRACERT, but not sure if that's very effective on a company network (depends on your size).
Ok, that's my two cents for right now, start a new post with what you've tried and any other info you can think of.....

Check the switch ports for runts. This is typically an indication of a duplex mismatch, which will result in this type of performance problem. Since the switch ports are set to 100 full, double-check that the NICs on the W2K systems are also set to 100 full. If so, as a test, try setting both the NIC and the switch port to Auto Negotiation and attempt the transfer again.