Jared:
I was looking at the 53131A specs and the minimum input spec for 100MHz to 2.7GHz is -27dBm and from there to 3Ghz is -21dBm.
I guess actual levels would be less than that , but not significantly or Agilent would have taken credit for it.
For the channel A and B inputs the levels range from 20mV to 40mV (-21dBm to -15dBm if terminated in 50 ohms).
Your board must have a lot of gain at the low end for the minimum input to be below -50dBm for frequencies below 800Mhz as seen in the PNG image you posted.
Like you, I also noticed that the input protection diodes affected the signal levels. More effect than I expected.?
I am currently using two Mini Circuits ERA amplifiers for the gain stage with a 3dB attenuator in line with the input.
My minimum input levels from 750MHz to 3GHz are somewhat in line with the Agilent spec, -34dBm to -21dBm.
At 500Mhz, the input level drops to -13dBm, I think my input cap and those in line may be too small.
ed