When you say you feel it at the top of the stroke, do you mean that the crank side arm somewhere between the 10 and 12 o'clock position?

This may or may not be it, but I had a similar thing last summer that drove me nuts for a few weeks. It turns out my crank arm was hitting the front derailleur cable. It didn't do it on every stroke, only when there was enough torque to flex the bike frame ever so little.