Hello Geoff,
So I would say the 5V is fine, your Arduino is working as what is on the display is coherent and at least a set of digital output are working (as they drive the display).
From what you say it seems that there is an issue with the controls section as labelled on the Raduino schematic.
I would concentrate on the wiring from the Raduino connector to the encoder and plugs.
Can you check that the encoder voltage change is seen on the connector on the Raduino too.
If you have the possibility of installing the KD8CEC software it has an analogue input monitor function. This would tell you a fair bit as to what if anything the Raduino is seing on its control inputs.
Hope that helps,
73, John (VK2ETA)
