I must agree. I think it sounds like a layer 1 or layer 2 problem. Swap out the cables on both PCs and see if the performance improves on the transfer.
Most of the time if the duplex setting and tranfer rates are set to auto they will negotiate the most optimal settings. Is there a delay when you ping between that machines? I mean outside of the normal LAN delay?
How many protocols do you have bound to the card? In most cases it should just be TCP/IP, but I have seen problems where people had Appletalk, IPX/SPX, TCP/IP and every thing else under the sun. Additional traffic from these protocols may cause delay.
Let me know the above info and ill see what else I can think of.