Hi Peter,
Yes you're right, I did reach out to the Nouveau mailing list. So far I haven't received any replies on that. I have spoken in #nouveau to "imirkin" and he has not had many ideas. He poked "skeggsb" about it, but never received much of a response from him..
I have only one monitor connected currently. I'm 95% sure that you're right, this is the GeForce 6800 Ultra DDL. Thanks for that link, pretty interesting stuff. This machine is neat because it is kind of a unicorn, but clearly that is causing me trouble with nouveau.
I tried your suggestion of booting with nouveau.duallink=0. That didn't help and I still got the Xorg.log message of both DVI outputs being connected. Here's my current Xorg.log:
Please please please keep the suggestions coming if you have them!
Logan