Let us know what the fitter says.

My gut on what you're feeling:
- seat may be low, or nose-down, causing the biomechanics of your stroke to have a dead spot
- you aren't used to clipless, and so don't pull up as part of the stroke, or you pull up and puch down but the transition is clunky
- too low on the cadence
- loose cleat, pedal, spindle or BB

Fitter should spot it pretty quickly.