If able check all the connections to ECM as well, unplug check for corrosion reseat plugs/wires/grounds.
Faulty ELD(Electronic Load Detector) may display this symptom also and there may actually be a TSB on it for your vehicle as there was for a lot of Honda's. I have also seen new alternators out of the box not up to snuff. A battery that is on it's way out(faulty cell) or bad connection could cause the fluctuations you see. You say the battery is good and charged, if you measure voltage at the battery(cold) it should be 12.4-12.6+ to be good(maybe have load tested). 13.7 V is OK when engine running and alternator putting out charge. Wli98122, When testing the voltages for battery/alternator test directly on clean battery terminals when possible. Am speculating that there might be an ECM component intermittent, but am loath to do a blind replacement without a specific cause.ΔΆ006 Honda Element with 102,000 trouble-free miles
The vehicle runs normally, the battery is good and holds a charge, and in all other respects the car acts as it should. Mechanics have installed another good alternator, serpentine belt, 100A fuse and B+ thick red wire with no change in reading behavior. The Honda charging circuit is simple: the B+ thick red wire goes directly to one lug of a 100A fuse (#19 under the hood), the other lug goes directly to the battery. My interpetation is that when it was reading 12.1, that was merely the battery voltage. None of the warning lights come on at any time. When driving the readings were 13.7v most of the time, BUT once every 2-3 hours, the voltage would drop to 12.1v for five-ten minutes before rising back up to 13.7. Mounted a known good VDO voltmeter tapping into the ACC fuse slot in the underdash fuse box.