I have a Foxconn Flamingbird, the BIOSes are maybe similar. Sometimes, if my memory clocks are too high, it also just recognizes one memory channel. Thus try with a lower RAM multiplier.
I hope you didnt forget that you overclock your RAM automatically when you are doing QPI-OC. Try the lowest, (DDR3-800) for a start.
Thanks for the tip, I do have two channels working, not just one. I relaxed the timings and downclocked the frequencies in my original 3x2 GB triple channel RAM. So much that it was slower than the 2x4 GB I replaced it with. At that point I just wanted to get the original RAM out of there because there was little reason to keep it (the benefit of an extra channel in that circumstance not being significant).
I also performed all the other typical trouble-shooting steps, like increasing Vtt.
I also moved parts around as well - and with a good i7-920, good sticks of 3x2gb and 2x4gb, and two LS 5639(s) - there's a lot of those tests you can make.