"Low battery" could be just that, a low battery. My VHF kept displaying low battery even after putting the charger on it over night it would still read "low battery" and the charger would read "CHARGED". I took the word of the VHF and replaced my 5 year old batteries and now the radio works fine.
Speaking of the CHARGER, guess what? There is something in that unit that totally screws with the fluxgate and puts the compass way off course and it affects the compass from almost anywhere on the boat, I have to take it off the boat and now I will have to go out and re-calibrate the fluxgate.
Oh yea, I have the RayMarine ST4000 MKII+ and it still works fine so I don't want to replace mine either. Have you tried locking the clutch lever into place, the one on the steering wheel disc? That will engage, dis-engage the the autoplilot lock. If that is not the problem search around your boat for some electrical appliance or cable that might be affecting the compass. The ST4000+ was and still is a solid product and you would be better off if you could trouble shoot the problem and keep it.