Thanks Kleinstein ... I explored this idea a bit.
I managed to power up the board on the bench with +/- 17V and the +5V relay power, and it behaved pretty much exactly as expected, I saw 4mV at x100, and 40mV at x1000 which all seemed nicely within tolerance and ruled out any issues with the jfet.
However, once back in the 5440B, at standby (which should be x100 shorted inputs) I was getting 250mV ... took me ages to figure it out [note to self: use a scope as well as a dmm], but it was ultimately a couple of electrolytics I hadn't yet changed on the PreAmp board, whenever that board was plugged in I saw over 500mV of noise/ripple on the 17V supplies.
There were three caps I changed, one for the oven circuit which was definitely faulty, but didn't improve things, but then when I did the two on the 17V supplies it all cleaned up nicely.
The analog tests still fail, but further on now at M33, I'm getting -7.7mV instead of something +/- 1.6mV, this is to do with the HIGHV INTCAL and seems to be pointing to a problem with the sample string PCA.... job for tomorrow!
EDIT: Problem solved ... M33 got me thinking back to the similar problem I had when I had one of the sample string relays making contact incorrectly ... a quick inspection of that replacement relay PCB for that relay and I found three pins on one of the relays that I hadn't soldered (rushing too much obviously!). With this fixed, the analog checks all pass ok, other than a sample string oven issue which I need to look into, and I'll wait until tomorrow to run the HV ones, end the day on a high.