A few suggestions:
1. Have you checked the status of the RAID sets? With some RAID 5 systems you hardly notice when a disk explodes!
2. Collision detection. If a collision detect circuit is bad, one machine may be "talking over" the others, which then have to retransmit.
If one machine appears to be in worse shape than the others, check the wiring on that one first - wiggle and bang the connectors (tech-talk) - then try replacing or swapping the cables around to see if the problem moves. Failing that, you could try swapping the network cards around.
The only sure way would be to use a network analyser, but 100Mbit hardware is not cheep. There may be some software solutions around that could be run on a "spare" machine with a 100Mbit card set to "promiscuous".