The wheel is a Speedcific Perception hub, 24 holes, radial lacing, IRD Niobium 31 rim.
When I spin the wheel while holding on to the axle ends, there is a definite "thunk." No noise, just something that feels like a bump is being hit inside the hub. (The wheel is almost perfectly true.)
Split bearing or a bad ball in the bearing will both cause this problem. So will a bad spot in the bearing race. It almost has to be a bearing because there is nothing else in there except the axle and it isn't moving.