you probably need to confirm a few things first.
check the voltage at the sensing wire for the voltage reg, the car can be in run, but doesn't have to be running.

see how close it is to the battery voltage.

use the battery for ground on battery, but use the case of the voltage reg for ground when you check voltage there.

if there is a difference then use the battery as ground and see if it goes away.
if not then I would be looking at the bulkhead connector and tracing it back to the ignition to see where you lose the voltage.

if the difference went away when you changed to battery ground, then the vr isn't grounded properly.

If it matched battery voltage, and you know this vr is good, then I would be getting the alt tested.