Have you tried the latest driver? http://downloadcenter.intel.com/Detail_Desc.aspx?DwnldID=17509
Your connections that go to the switch are working, so this seems related to running the back-to-back connection. You said that you tried both straight-through and a crossover cables. How about trying a longer cable? Have you tried throwing in a switch in between the two connections to narrow things down to confirm whether the issue might be caused by the back-to-back connection or not?
I noticed this issue listed in the readme:
Detected Tx Unit Hang in Quad Port Adapters
In some cases ports 3 and 4 won’t pass traffic. Ports 1 and 2 don't show
any errors and will pass traffic.
This issue MAY be resolved by updating to the latest BIOS. You can
check your system's BIOS by downloading the Linux Firmware Developer Kit
that can be obtained at http://www.linuxfirmwarekit.org/
So making sure you have the latest BIOS updates (if any) is worthwhile.
If none of the above helps, try sending an email with details about your issue to firstname.lastname@example.org.
We have not tried the latest driver yet as this would require recompiling the kernel.
We have tried a variety of cable and lengths with no joy.
We have just tried plugging the fourth interface igb3 into a switch and VLANing them off and the connection remains with no drops. So it looks like the problem is the direct connection between the two NICs.
We are running the latest firmware(BIOS) for the NICs.