troubleshooting Question

Two Identical HP Servers, One Has Very Slow Network Speeds

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compsol1993 asked on
Server HardwareStorage SoftwareMicrosoft Server OS
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We are running two HP Windows 2003 Server Standard Editions.  We backup both over the gigabit network from a third master server, a slightly newer Dell server.

Server_1 is identical to Server_2 except Server_1 has 2 GB of ram, Server_2 only has 1 GB.

Server_1 is backing up at a rate of 2 MB/min.
Server_2 is backing up at a rate of 350MB/min.

As you can see, Server_1 is running much slower over the network.  Here is what we have done so far:
-Rebooted servers and all network hardware.
-Swapped network cable on Server_1 and Server_2.
-Connected Server_1 to a different network switch
-Replaced network card on Server_1
-Stopped all Antivirus/disabled firewall on Server_1

None of these factors has changed the performance of Server_1.  Looking back at our logs, this has been a consistent problem since November 2006, possibly further back.  

We have looked over the process lists, and do not see anything different between the two servers except for some proprietary software we are running.  Stopping this software does not affect performance.

So, does anyone have any ideas on what we should look for as the problem.  We feel pretty confident it is not a malware problem, but are willing to consider it if someone has any advice.  Several virus/spyware/rootkit scans have determined the computer is clean.  We are not seeing any typical signs of a malware infestation.

Also, when we copy a 900 MB file to that server, over the network it flucuates in the time it will take to complete.  Such as:
5 minutes remaining ...  50 minutes remaining ... 10 minutes remaining ... 67 minutes remaining
Copying the same file off of the machine seems to yield a rate of at least 200 MB/min, so the problem appears to only be related to incoming traffic.

Thanks for any advice.
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