The simple standard set up for an alternator is the sense wire is connected to the positive system. It "reads" system voltage. Low system voltage means higher alternator voltage. As the alternator charges the batteries the system voltage comes up until the alternator is "trickle" charging
the system with just a slightly higher than system voltage.
The location where the sense wire picks up system voltage is important. There are a few theories on this. Some say put it near the battery. However if the battery is close to the alternator you may not be reading what the bus is seeing if the bus is "far" from the battery due to system losses. In a car this is important because we are generally consuming what we produce in this always on system. Sensing at the battery with deteriorated conenctions to the bus often can result in dim headlights.
In a boat, however, we are interested in topping up the batteries. So a sense wire onthe battery might make sense.
I hedge my bet and like the field pick on a lug between the battery and the bus - as equidistant as I can make it.
So - One alternator may be seeing a different system voltage than the other. Cause could be hookup location or clean vs. dirty connections, loose vs. tight connections etc.
If you have a charge controller, the internal function of the sense system is taken over by the controller to essentially charge at a higher rate for a longer period. So in this case your problem could be a lot more complex.