I'm running 2 6990s (both with the OC switch on the overclocked position, but no further OCing) on a single-core Sempron 140. With cgminer, one card gets the expected performance, but the other one is incredibly low (40-50Mhash per GPU). I'm using an intensity of 9 as suggested in the original post for 6990s.
This is the exit output:
GPU 0: [395.7 Mh/s] [Q:91 A:85 R:3 HW:0 E:93% U:5.55/m]
GPU 1: [395.6 Mh/s] [Q:92 A:96 R:1 HW:0 E:104% U:6.20/m]
GPU 2: [39.4 Mh/s] [Q:12 A:5 R:0 HW:0 E:42% U:3.13/m]
GPU 3: [46.4 Mh/s] [Q:13 A:10 R:0 HW:0 E:83% U:5.95/m]
Your CPU might be the limiting factor. Take out the card that is performing as it should and see if the second card performs normally or not. If not, try installing that GPU where the one that was performing normally was. If it performs as it should, then that card is being installed into a lower bandwidth PCI-E slot (not all full length slots are 16x wired, check your motherboard manual). If it still does not perform as it should then you may have a defective card.
Edit: Power supply could also be an issue, what brand/model and how many watts?
Hope this helps.