Ahh the sweet smell of success. Simply replacing the cable with shielded cable did the trick. I had to do a little bit of poking about with the pulley speed setting to get the intermediate values to fall into line, but now they all agree within around 20rpms. Thats good enough for me.

Thanks JAZZ and Clive for all your help.

BTW Clive there is no daughter board, the BOB has the PWM output directly on the board.