Abnormal Signal Values on Beacon Receiver

If your beacon receiver is giving low signal alarm I would immediately check to see if the wanted traffic is also low level.

Are you still receiving the normal wanted traffic signals from the wanted satellite ?

If RX traffic is OK, I would put the AUPC into manual mode and reduce the BUC/HPA power and transmit EIRP to normal level, assuming clear sky conditions. The NOC will then stop complaining that you are transmitting 6 dB too high. If your uplink bandwidth occupies a significant proportion of a transponder your excessive transmit power may cause many other customers to lose service. You will also cause uplink and downlink cross-pol interference.

If all RX traffic is gone, turn the transmit OFF and check the LNB and antenna az-el pointing. Switch to redundant LNB or re-point dish, as required, to regain wanted satellite and restore service.

If you have a problem associated with just the beacon receiver and its input cable, set the AUPC to manual and set normal transmit level while investigating. Consider using spectrum analyser to see if the beacon signal still exists at the expected frequency and level on the cable at the beacon receiver input.

A general bit of advice about beacon receivers, tracking receivers and AUPC.
It is important that the whole system is linear. Problems I have encountered are: 1. Excessively high gain LNA/LNB with large antenna pointed at satellite with TV carriers intended for small home dishes.  Symptom: Antenna pattern did not look right and intermodulation on RX.   Cure: Low gain LNB so its output stage transistor was not saturated. 2. Excessively high input level to beacon receiver. Symptom: Tracking did not peak up properly. Cure: 30 dB attenuator on beacon receiver input.
It is essential that 1, 2, 5, 10, 15 dB reductions of signal level into the dish cause identical matching changes on the beacon receiver display and in the scaled analogue voltage output. Adjust things so that the clear sky output voltage is towards the upper end of the whole working voltage range.

A general bit of advice about peaking up the dish pointing on a large dish.
Once you think you are pointed at main beam peak, move the dish about sideways and check that you see first sidelobes either way. They should be about 10 to 15 dB down and similar level to each other.
Repeat in elevation. All four sidelobe peaks should be similar. See https://www.satsig.net/sub-reflector-alignment.htm
If you ever see what appears to be two main beams move to the hollow or small hump between them and change direction and see what happens. You were peaked on the first sidelobe!

Check for loose connections on cables from L band splitter to tracking receiver input.

Look with spectrum analyser on the cable end at the beacon receiver for any signals. What is the exact frequency of the beacon ?

If you get it working waggle all the cable connectors to try and identify any intermittent terminations.

Check configuration of beacon receiver. Cycle the power. Is input B configured, with cable input plugged to socket A ?
Does the beacon receiver have a frequency tracking capability ?  How wide will this go ?  Has the LNB local oscillator drifted too far ?  Are you using an internal or external PLL type LNB ? Is it locked ? Is the 10 MHz supply working ?

I agree it is beginning to look like a beacon receiver hardware fault.

Some suggestions.

. is the monitor port level supposed to be -20 dB relative to the main input? The beacon receiver manual should tell you.  -20 dB might well be correct, but alternatives like -10 dB or 0 dB difference are possible.
. is the input B socket damaged? If the center pin of the plug is too long it can break the socket to printed circuit board connection inside.
. are you using a 50 ohm plug into a 75 ohm socket, or vice versa.
. is DC power present on the cable.
. why was input B ever used?   Was input A faulty or damaged a long time ago? Try using input A instead of input B.
. check the configuration of the beacon receiver, e.g. bandwidth, search range. It may have lost lock on the signal due to frequency drift if the frequency tracking function was turned off or not wide enough.
. the beacon receiver may have more detailed fault/alarm diagnostics. Are its power supply voltages all correct?.
. try applying a CW test signal direct to the beacon receiver, inputs A and B.
. connect the beacon receiver direct to a point nearer the LNB output.

Your spectrum pictures have the resolution bandwidth at 300 kHz. Try 30 kHz or 3 kHz RBW.  The 'beacon' may be a central CW carrier with telemetry sidebands or just a clean unmodulated CW carrier. This might affect how the beacon receiver is intended to work. It needs to lock to the central CW carrier using a narrow bandwidth or measure the entire signal using a wider bandwidth.

Maybe contact the beacon receiver manufacturer ?