12 volt Aux Battery readings different on voltmeter vs display in ACC mode

No fix. You measured the battery with a larger load vs smaller load, volts drop in proportion with load. .

 

welcome!
how old is the battery?

 

Following @bisco's advice, I've found a drop of maybe 0.2 volts, measuring the voltage with a digital meter, the following two scenarios:

1. First thing in the morning, with the hood left ajar the night before. (measurement: 12.9 volts)
2. First thing in the morning, but opening front passenger door momentarily, to pop the hood. (measurement: 12.7 volts)

In other words, anything that wakes the car can drop the voltage, and make it remain lower, even minutes afterwards. So having the car "on" or in "accessory" mode, is for sure going to skew the readings.

 

One thing is that the nav headunit is measuring its own voltage: that is, the voltage that reaches it, coming from the battery, through fuses, relays, wires, and connectors, into the nav headunit itself, to whatever place in the circuit it actually measures the voltage.

All of those intermediate bits (fuses, relays, wires, connectors) have voltage drops that all add up, and the drops are proportional to the current flowing over them. The connectors and paths right at the nav unit are carrying only the nav unit's own current, but the ones more upstream are carrying more, because they are shared by other circuits that branch off.

For years I've been using the rule of thumb that the voltage shown on the nav unit can be around 0.6 or 0.7 volts lower than that fully upstream at the battery. It was that way in my Gen 1 also.

It's kind of a pain to get to the battery to do that simultaneous measurement. For another proxy, there is a pin at the DLC3 (diagnostic) port that just carries battery voltage, so a diagnostic tool can measure it. It is still downstream of the whole length of wire from the battery to the instrument panel, but not nearly as many fuses and relays on the path (it's always powered), nor other circuits sharing it to pull the voltage down.

The other day, I distinctly had my ScanGauge plugged into that port and the nav display showing volts, and the reading on the ScanGauge was exactly 0.7 volts higher.

I understand it's surprising, but it's also pretty consistent ... at least within one car, when you've learned what the delta is, it doesn't bounce around much. Maybe there is more variation between cars. The ones I've had have been pretty consistent.