If it's worth anything, my 780 did the same thing for awhile. It bugged the crap out of me. I got busy and kind of forgot about it, but then a month or two later when I remembered (actually when the intake holes on my case were accidentally covered and I noticed my computer getting loud as shit), I started running afterburner again while gaming and clocks would lock in at their max boost in the same games they used to fluctuate in. Nothing had changed otherwise besides new drivers (I'm assuming).
I think this may turn out to be a case of early maxwell drivers being a little finnicky.