It's possible that your Autohelm is fine, and it's just reacting to voltage sags, surges or spikes on the +12V power. Boat 12 power systems are notorious for being extremely noisy. My Raymarine wheelpilot will reset to standby whenever I start the engine. This is because the starter motor pulls an extreme load and causes the voltage to momentarily sag low enough to cause the autopilot to drop out. (The cure for this, by the way, is a dedicated start battery...its on my "to do" list...).
Other sources can also produce sags and surges on the power bus, though not as extreme as the starter. Keying the VHF for transmit, running the windlass, or running anything with a motor, such as a blower, fan, or refrigeration, can all put varying amounts of "noise" on the 12V power buss.
A simple test to see if this is your problem would be to temporarily run the Autohelm off of a small dedicated 12v battery. A little gel cell, such as those used in lawnmowers or home alarm systems, would be ideal. It can supply enough current to run the Autohelm for a while, and is safe to handle, with no danger of acid spillage.
If this cures the problem, a permanent solution would be to install an "LC low-pass noise filter" on the power lead to the Autohelm. There's a useful discussion on a DIY solution in stackexchange:
http://electronics.stackexchange.com/questions/71698/diy-protection-for-12v-electronics-wired-directly-to-a-marine-12v-battery-system