The 27kHz line in the green locking was from the polarization controller, as Bram suggested.  Attached are plots of the PLL and PDH error signals with the MPC powered on and off.  

There is also a wandering feature in both signals that goes away when the MC is unlocked.  

Again this afternoon the single shot cavity alignment was good, but the dither alignment kept arriving at an alignment where the cavity axis was different from the single shot beam.