I was eventually able to get this working by moving the card to the very last slot (furthest from the CPU) on my x9scm motherboard.
This is probably related to slot 4 being the only physical slot connected to the Cougar Point PCH (see Supermicro's documentation<http://www.supermicro.com/manuals/motherboard/C202_C204/MNL-1270.pdf>). I'm not sure why exactly this is the case, but perhaps this will be solved in a future bios firmware update. I sure hope so because I intended to use more than one quad port NIC with this motherboard.
Hope this helps!