Where have you found the -0.8 and -1.6V ? Because on the schematic p327. both are -1.6V.
This is "standard" ECL and the signals clearly need to be complementary in that circuit, as this is a current switch.
On the page 84 (Ramp switching) is said that during the calibration, the JIT1 GAIN is applied to the base of Q495, but i can't see any signal, only a DC value of -5.2 V during the normal operation or Repet Cal or Self Cal. And the MUX U651 (FO12 p.311) driving this BJT through U661A doesn't provide any kind of signal on all of its outputs (except one, with -1 V DC which is strange), whereas all input signals seems to be ok.
The signal is a DC signal, though it may wobble a little during self cal.
Basically the DC voltage on the transistor decides how much current the slow "drain" current sink sinks. This in turn decides the time expansion ratio, and ISTR the service manual wants a ratio of 1250 between the fast and slow ramps.
Otherwise while the scope is stuck the output of the comparator U490 is 0 V, compared to 3.56V when it works
How are you observing this - are you using an oscilloscope or e.g. a DMM?
This sounds reasonably salient, though only if the ramp is also running, and this is a difference only in the output and not in the inputs. If the inputs to the jitter ramp are static while the scope is stuck, you need to look further "upstream".
Interesting questions to ask and answer relate to how much of the digital circuitry is operational when the scope is stuck. We want to try and isolate the problem to a block in the block diagram or to a device in a schematic.
Since you have intensity control, it seems the FPP works when the scope is stuck.
I believe the intensity signal comes through the DAC and a mux from the MCU. This implies the regular interrupt works, the DAC works and the multiplexer in question works.
Can you check those and report back?
Can you post a video where you exercise *every* front panel control while the scope is stuck?
In particular exercise the vertical channel controls and listen for relay clicks. Exercise the coupling controls and listen for same.
Try shorting the BNC input sense ring to ground, and/or plugging in a 10X probe, see whether anything changes in the readout, and so on.