Device Manager should detect two R9 200 series card. this is a mobo with 6 cards:
if only one card is showing up, that's why cgminer only is mining on one card. it means it's a windows or a hardware problem.
try swapping the cards to eliminate defective card.
you can also determine if the issue can be blamed on the pci-e x1 and/or riser. try running the pci-e x1 card and open x16 slot to see if you can force windows to recognize the other card.
what kind of motherboard is it? lots of pci slots.