Ok, controller ruled out 😊
Where were you measuring the battery voltage from with the meter, from the charge port or the two outer pins from the connector on the battery? A 48 volt battery at 100% is 54.6 volts, but the Rad charger usually gets the battery up to 54.4 - ish.
Charge the battery up with the Rad charger until the green light comes on, disconnect the charger, then measure the battery voltage at the terminals after 15 minutes. If it measures low, below 50 volts, then your battery may be bad. If the Battery voltage measures full, between 53.8 and 54.6 volts, then contact Luna about a possible problem with the charger. They will probably walk you through a few tests.