The MacPro 3,1 onboard NIC (or more precisely, the built-in Intel driver) is known to drop ethernet connections.
This may not be exposed during normal network operations, but iSCSI uses much more of the available bandwidth, and we've found it happening very frequently on these machines as people upgrade their OS.
The good news is that adding a relatively inexpensive ethernet adapter that uses a different driver is an effective workaround.
We've recommended cards that will use Apple's built-in Yukon driver rather than the Intel driver, and found this to consistently fix reported iSCSI drops on 3,1 workstations.
We've personally tested with this card, and have had customers report success using Sonnet's Presto Gigabit Pro or Presto Gigabit Server adapters.