J. Freed
Found the problem discribed in 90644, as well as the strange sawtooth beat notes we have been finding in our IFOs. It was user error on our CDS system, the double mixer (which produces our REF RF signal for AOMs) requires a sin wave and cos wave 4096Hz signal. We were sending it 2x cos signals.
This also explains why our demod systems were not working as they use the same signals.
The sawtooth that Josh mentions was how the poorly phased analog versions of the 4096 Hz SIN and COS LO signals manifested on the digitized versions of the IFO PD voltage, reading out that beatnote. Here, I attach what it looked like on the o-scope (before discovering the issue of phasing the two SIN and COS versions of the LO).