I have 4 M18x Alienware systems with Dual 6990s. They get VERY different results.

I have redone drivers, OS, updated the firmware on all the systems and done a direct comparison, even went so far as to take an image of one system and put it on the other.

http://moowrap.net/host_app_versions.php?hostid=7309

http://moowrap.net/host_app_versions.php?hostid=7859

Anything I can check?

Hello..IMO, the duel gpu's in each rig is your problem..most likely. So take one out of 1 or 2 rigs and see what you get. Basicly duel's cut your gpu's in half. There are ways to use each one on a single wu(I think)but I am not the one to help you on that. I would scower the msg brd and or PM Teemu. One 69xx should bring easly 450K (very conservative figure) Also try just gpu'ing, no cpu's, what are your cores running?
Unless you already chaged something, rig 7859 times are perfect, the other rig is taking triple time.
Use GPU-Z to see what the cores are doing. Also what CCC are you using? Any OCing? 69xx do not like to be OCed, well not much head room.
Look at "Number crunching, ATI 12.1 - Preview" on the same brd yours is.

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It's in the laptop, so I can't just take one out.

I am overclocking all 4 systems I'll take that back to stock and see what it does.

Opps..I looked it...WOW what a laptop, nice..The tower I could have built with that $2000 :)There is a way to make Moo use only 1 gpu, I kinda know how, but I would not want to steer you in the wrong direction. Theres a xml. file in your Boinc/Moo folder and a setting you can change. Stock clocks would be best!

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I am overclocking my 6990's to gpu 900 memory 1350 - stable. The issue with the dual cards is cooling, I removed the side of my case, and put a piece of cardboard in its place, with 2 140mm fans blowing on the cards, and an airdam forcing most of the air on the cards (and keeping all hot air out of the cards fan intakes). I am running 55% fan speed at 85 / 81 degrees on milkyway, 54% 76 / 71 degrees on collatz, 52% fan 74 / 72 degrees on Moo. There seams to be no rhyme or reason to the valid units, the invalid units seem to be a 1 out of x, no matter if I overclock or not. If you don't already have it, get MSI's Afterburner, if nothing else you can easily watch the status of your cards. I made up a custom cooling curve to limit temps (to 88 degrees max) and reduce the fan noise when cooler then that.

I am overclocking my 6990's to gpu 900 memory 1350 - stable. The issue with the dual cards is cooling, I removed the side of my case, and put a piece of cardboard in its place, with 2 140mm fans blowing on the cards, and an airdam forcing most of the air on the cards (and keeping all hot air out of the cards fan intakes). I am running 55% fan speed at 85 / 81 degrees on milkyway, 54% 76 / 71 degrees on collatz, 52% fan 74 / 72 degrees on Moo. There seams to be no rhyme or reason to the valid units, the invalid units seem to be a 1 out of x, no matter if I overclock or not. If you don't already have it, get MSI's Afterburner, if nothing else you can easily watch the status of your cards. I made up a custom cooling curve to limit temps (to 88 degrees max) and reduce the fan noise when cooler then that.

I think your problem is your version of the software, you are running HIGHER than 11.9, your version is driver: 1.4.1664 while 11.9 is driver: 1.4.1546. The newer ones are good for gaming but not for crunching. AMD is making changes that are not benefiting us crunchers!

I'll do a driver roll back on two of the four and capture the results for a few days.