Well apparently there was a power outage over the weekend that I wasn't aware of. Perhaps that has something to do with the issues. Either way on a whim I shut everything down and plugged the second Chili back in and for the past 45 minutes now they've both been cruising. I do find it interesting that when I was just running 1 it ran about 3GH/s faster though. Will they dynamically adjust their speed in response to a power shortage? Or to put it another way - is it possible/likely that the Chilis have the ability to run at a slower speed if they sense they aren't getting enough juice to really push things?

It shouldn't be a heat issue - one is air cooled and the other is water cooled and they're positioned in such a way that they shouldn't be sharing any warm air.