zizou, my first guess would be weight distribution, before aero spokes and wind depth creating turbulence. are you further forward on your track bike? steeper seat tube angle?
also, some people attribute rear-wheel-skip in a sprint to an uneven pedal stroke. you push down but when your crank is at 6, if you don't pull up in time - if you're just the slightest bit out of sequence - then you wind up pushing down, effectively lifting your body somewhat (as if you were starting to stand up - micro movement) and then when you do lift back up, you lift your rear wheel a tiny bit.