Ha, ADC module is from Keithley 2001. Nice.
You may want to draw simplified signal diagram for high voltage path, to find suspected parts which can cause your issue. Its likely something on output stage.
So you check CR304,CR305,C311-313,C315-C317 and they have -1200V/+1200V on VR303,VR304?
Check if VR311 anode have -1200V too, when set voltage source to 100V and operate is ON. U308 pin 4 should have 4.81V. Measurements against V Source Lo.