The slots definitely work as I tested them with a different card (9207-8i). The OS is the same too.When I've had issues like that (although usually in consumer boards) SOMETIMES taping the two SMBUS connectors does the trick. You'll need some katon tape or similar, have it wrap *slightly* around the bottom to keep it from peeling off as you insert it and have it go up the card enough so it doesn't get stuck in the slot when pulling it out.
If that still doesn't work make sure you are using the same os on both boards to reduce variables, check that the slot works at all, and look in bios/eufi for any possible conflicting settings.
I could not find anything that I would want to try changing in the BIOS settings.
I'll check out the SMBus trick.