I will try to find some time to revisit my board and make a graph of its sensitivity vs the Agilent and we can compare.
I am using the MC12079 prescaler and two Mini Circuits amplifiers so it is a bit different.
Never had a real prescaler board from HP/Agilent to compare so not sure if the OEM board has the input problem, but I would guess not.
I had added a comparator and 74LVC1G17 buffer after the prescaler chip and that may be part of my problem.
The 53131 does not need the 5V signal, the output of the prescaler chip should be enough, so I will jumper those out and see what happens.
ed