I was double checking the UGF of the PLL and was getting the strange results of 8 kHz UGF with the standard settings of 10 kHz/V and SR560 set to 23 dB gain (Marconi was set to +13 dBm RF power level). In the past we got 30 kHz for this configuration.

Since then an acromag channel was connected to the same 600 Ω output of the SR560 as the Marconi signal generator. This was to monitor the state of the PLL loop so that the Marconi center frequency could be adjusted (through GPIB and a python script) to always have the PLL locked.

It turns out that the acromag channel monitoring the BN DC level is overloading/lowpass filtering the 600 Ω input. Attached below is a transfer function of the SR560 with 2x100 gain setting (no filtering): here the BN has been disconnected this is just the preamp itself. With the acromag connected it appears to add a pole at 3 kHz. This will have changed the PLL loop response in recent measurments.  

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I have now moved the acromag to the 50 Ω buffered output of the SR560, reported voltages should be the same (acromag is high impedance) but the loop now has the expected 30 kHz as before.  Calibrations of previous week should be taken with a grain of salt.