I left the tester box plugged in from Thursday night to Sunday afternoon, and in this period, the glitches still appeared in (and only in) the UL channel.

So yesterday evening, I pulled the Sat. Box. out and checked the DC voltages at various points in the circuit using a DMM, including the output of the high current buffer that supplies the drive current to the shadow sensor LEDs. When we had similar behaviour in the PRM box, this kind of analysis immediately identified the faulty component as the high current buffer IC (LM6321M) in the bad channel, but everything seems in order for the ITMY box. 

I then checked the Satellite Amplifier Termination Board, which basically just adds 100ohm series resistors to the output of the PD readout, and all the resistors seem fine, the piece of insulating material affixed to the bottom of this board is also intact. I then used the SR785 in AC coupled mode to look at the high frequency spectrum at the same points I checked the DC voltages with the DMM (namely the drive voltage to the LEDs, and the PD readout voltages on the PCB as well as on the pins of the connector on the outside of the box after the termination board (leading to the DAQ), and nothing sticks out here in the UL channel either. Of course it could be that the glitches are intermittent, and during my tests they just weren't there...

I am hesitant to start pulling out ICs and replacing them without any obvious signs of failure from them, but I am out of debugging ideas...

One possibility is that the problem lies upstream of the Sat. Box - perhaps the UL channel in the Suspension PD Whitening and Interface Board is faulty. To test, I have now hooked up ITMY Sat. Box. + tester box to the signal chain of ETMY. If I can get the other tester box back from Ben, I will plug in the ETMY sat. box. + tester to the ITMY signal chain. This should tell us something...