I had noticed in the past, that the digital control signal monitor for the X end would saturate well before the ADC should saturate (C1:ALS-X_SLOW_SERVO_IN1, which is from the "output mon" BNC on the box). It turns out that there is some odd saturation happening inside the box itself.

In this scope trace, the servo input is being driven with a 0.02Vpp, 0.1Hz sine wave, gain knob at 1.0. This is bad. 

Evan and I poked around the board, and discover that for some reason currently unknown to us, the variable gain amplifier (AD8336) can't reach its negative rail, despite the +-12V arriving safely at its power supply pins. 

I also realized that the LF356 in the integrator stage in this box had been replaced with a LT1792 by Kiwamu in ELOG 4373. I've updated my schematic, and will upload both boxes' schematics to the DCC page Jenne created for them. (D1400293 and D1400294)