First, make sure the cards are on the tested list at http://serverconfigurator.intel.com/sct_private/sct_app.aspx#/SctTHOL/21320/Intel%C2%AE%20Server%20Board%20S1200BTS%20%28S1200BTS%29
Also, the different slots enumerate differently. Try one card at a time, and try them in different slots.
I had a similar problem but I never figured it out. Tried the latest drivers (from August) to no avail. I actually couldn't get it to recognize any PCI / PCIe devices at all. I tried all slots on the MB and I tried it on 2 different MBs - both identical S1200BTL, both with the same identical problems. Everything else worked. I was never able to find an adapter for the PS/AUX 5-pin connector on the MB (a rather obsolete connector, not sure why they used that one) - could that be why?