Are both machines on the same switch/router?
Is there a firewall between them?
Have you verified that both network interfaces are set to 100Mb/s Full-Duplex?
Are you able to view the logs of the switch/router to see if there are errors on the ports that the two machines are plugged in to?
All of those were troubleshooting steps that I took within the past couple of weeks to determine why one of my servers had a dramatically slower throughput speed when doing it's nightly backups to tape. It turned out, that the switch port was seeing massive numbers of errors that we finally linked back to a mismatch of NIC settings. Both NICs were set to autonegotiate with the switch, but one was getting 100Mb/s Full and one was getting 100Mb/s half and sometimes even 10Mb/s half. After I forced the NICs to 100Mb/s Full, my throughput increased from 157kb/s to over 800kb/s, and now backups that were taking close to 8 hours take less than 1 hour.