Maybe reducing power to the fans is stressing the MB somehow. I did notice non-PWM fans can squeel like they are stressed.
I think the Diode it is on top of the 4 in the word SATA3G_4 here...
http://www.flickr.com/photos/pc-actual/6073540748/in/set-72157627376563753/Clear any cables from this area. Make sure you graphics card does not make this area hot when the waterloop fans slow. Make sure the GPU is not leaning on the ROG heatsink (when you screw it into the slot lean it away from the ROG cover.
When I fan this spot by hand with a small fan it drops the MB temp reading, so I think it is actually the temp.
Oh I think Raja said MB chipset is fine with high temps... but obviously it is not great. You might find it is best to exhaust the top of the case with a silent fan on low speed, just to stop stagnant areas building up temps. Depends on the case but one exhaust as high up as possible is best, the PSU can do it if it does not switch its fan off. For a desktop case two low speed fans on the CPU side with static proof plastic dividers making a duct from the CPU to one of them is best.