Not fully charging batteries

[Bengy88]

You need to make sure the batteries in the apu arent AGM. This is a common ussue that goes unseen and alot of times unknown. When an apu is installed 90% of the time agm batteries are installed but the standard flooded batteries are left in the truck. If the batteries for the apu are tied to the batteries in the truck in any way then the batteries are working against each other (i guess thats the best way to put it) agm batteries hold about .3 to .4 volts over a standard battery...... But thats not your problem

But with what your saying about voltage spiking then dropping i would be checking my alternator output versus voltage at batteries