I'm very much confused by the labeling of your graphs.
Graph "No1":
The X axis runs from under 55 to over 70 and is labeled "run time (milliseconds)". It looks like you may have meant "(seconds)".
The "setpoint/programmed voltage" line has some major spikes and appears to step about once per "millisecond" (second?).
The blue line is not labeled at all. There is an axis labeled "PID/output (a.u.)" What is an "a.u." in this context?!?
Graph"No3":
the X axis runs from about 5000 to about 7750, is labeled "run time (milliseconds)"?!?
The "XI-390 sensor signal (Volts)" rises from 0.0V at 5000 mS to level out around 1.75V at about 6500 mS.
The "setpoint/programmed voltage" is slamming between 0V and 3.3V about 24 times per second.
The "PID/output" seems to be tracking the sensor signal but ranges from 395000 to 422000.
The graphs are not going to help without at least a better description of where the data comes from.
It appears that you are using a PID loop to get a specific ramp out of your sensor. I suspect you are changing the setpoint too infrequently so the jumps in Setpoint cause a spike in Output. If it were me, I'd change the Setpoint as frequently as possible.