Ken Kundert

It is not clock feedthrough. The periodic small signal analyses all employ two steps. First, the clock is applied and periodic operating point is computed. From this a linear periodic representation is created. Second, the small signals are applied and the small signal response is computed. The clocks are only applied in the first step. In the second step, only the smallsignal stimulus is applied.
Thus, the ripples and peaks at the multiples of the clock signals are not clock feedthrough. They can be one of two things. They can be low frequency dynamics that are being mixed up to the harmonics of the clock. Or they can be cancellations from the various paths the signals take as the get mixed up and down by the clock.
I am not exactly sure how to interpret the Nyquist criteria on clocked circuits, so I don't know what to make of your results. However, I do know that one sure way to determine the stability of a feedback system is to simply perform a transient analysis and see if the circuit oscillates. You should force a small time step and stimulate the circuit with a very abrupt step.
Ken
