We investigate frequency correlations of low frequency (LF, <80 Hz) and kHz quasi-periodic oscillations (QPOs) using the complete RXTE data sets on 6 accreting millisecond X-ray pulsars (AMXPs) and compare them to those of non-pulsating neutron star low mass X-ray binaries with known spin. For the AMXPs SAX J1808.4-3658 and XTE J1807-294, we find frequency-correlation power law indices that, surprisingly, are significantly lower than in the non-pulsars, and consistent with the relativistic precession model (RPM) prediction of 2.0 appropriate to test-particle orbital and Lense-Thirring precession frequencies. As previously reported, power law normalizations are significantly higher in these AMXPs than in the non-pulsating sources, leading to requirements on the neutron star specific moment of inertia in this model that cannot be satisfied with realistic equations of state. At least two other AMXPs show frequency correlations inconsistent with those of SAX J1808.4-3658 and XTE J1807-294, and possibly similar to those of the non-pulsating sources; for two AMXPs no conclusions could be drawn. We discuss these results in the context of a model that has had success in black hole (BH) systems involving a torus-like hot inner flow precessing due to (prograde) frame dragging, and a scenario in which additional (retrograde) magnetic and classical precession torques not present in BH systems are also considered. We show that a combination of these interpretations may accommodate our results.