TR-1 Gold issue

[Scalloper 1]

I bought a new boat in April. Its a 20.6 Duckworth. I installed a 99 Yamaha kicker with the TR-1 autopilot. I have 25 years of experience running APs on commercial boats. This works great but sometimes 3-10 times per day it goes into "Standby mode" and stops steering the boat. Some times to does it when I walk back to adjust the riggers and the boat tips slightly but many times it will go into stby when there is no movement aboard the boat. Any idea what could cause this? 

Note: I did not think to look at my voltage when this happens and I am only running one battery.