You already got 5 cards working on the 1000W PSU, correct?
Try unplugging all cards from the system and boot it up with a single card + riser on the 400w PSU and the motherboard on the 1000W PSU. That way you can isolate your problem and find out if it's the second PSU or a software issue. If the card doesn't show up something's wrong on the hardware side. If it works the issue lies in the software.