Important thing to note is the power wires coming from the ST-3000 drive motor are brown and blue. Blue is POSITIVE and brown is NEGATIVE. I found advice online that said opposite.
Geoff - You overlooked the obvious. Your boat is wired wrong.
The brown wire of the power supply
lead should be connected to positive. If
connections are accidently reversed the
Autohelm 4000 will not operate but no
damage will result.
This was copied/pasted from my Autohelm 4000 manual. It's always been the same. It's the Autohelm/Raymarine standard.
The wiring should be corrected before you get in trouble somewhere else.
Before I realized that you had solved your problem I was going to point out that most Autohelm connectors have screws fastening the wires to the terminals. If a screw comes loose you will have the problems you described. I'd tell you how I know, but it's time for a sundowner in the east.