Try lowering the diff on your 6990, even try multiple threads on a lower intesity. Yes you get a slightly lower hashrate (difference on my cards is like 5-10kh/s) but you get less stales and a higher return, at-least that's what I have found anyway.
Thanks for your advise.
However, I do need the high intensity because this rig is also CPU mining XPM.
If I cut intensity below 18 the hashrate skydives, unless I stop the CPU miner.
The 6990 does 950 Kh/s on I 19, with CPU miner enabled it drops to 915.
Any lowering of intensity has a dramatic impact on the hashrate. (I 17 gives 600-650)
So, thats why I'm reluctantly pointing it at a LTC pool. High hashrate, almost no rejects, and my CPU is doing something usefull.
Set CPU Miner to Lowest Priority in Windows or set the NICE value to 10 (using RENICE) for *nix to give your CGMiner higher priority. This should give you more breathing room.