If you are referring to the chassis alternator, check each cell in each of the batteries connected to the alternator. Then give each battery a "drain" check - put a known load on the batteries and check the voltage drops. A battery service center should be able to do this.
Check the actual voltage in the charging circuit at varoius points within the circuit. These points include alternator output, isolator in, isolator out, (the isolator "splits" the charge circuit to the house battery and the chassis battery), and the voltage at each battery (check both the terminal clamps and the terminal posts) while the engine is running.
If you are convinced the new voltage regulator is good, sounds like a wiring or battery problem to me.
Welcome to the Forums.
"Suck it up, spend the bucks, do it right the first time."
WBCCI # 1113
Trailer '78 31' Sovereign
Living Large at an Airstream Park on the Largest Lake Totally Contained in Texas
Texas Airstream Harbor, Inc.