Are you monitoring the clock speeds of your cards?
I had a weird thing happen with my 5850 a while ago when I was trying to apply settings in MSI Afterburner. When I would enter in a gpu clock amount, like 850, and press apply, it'd go up to that speed for a few seconds, then back down to the factory 725 speed.
Yea, I've been monitoring that and it's all good. I disabled power play plus emptied the "profiles", so there is no auto-switching going on. At any rate, I think it's just a personality trait; takes a couple of hours for my GPU to get up to speed, for whatever reason.