2003 F-250, new batteries. If it sits overnight, batteries dead by morning. Can unplug alternator and no drain on batteries. Two dealers have both checked alternator and pronounced it working fine. But it's draining batteries if left hooked up. Driving me nuts. Other owners report same problem. Any suggestions?
Just to verify which wire you disconnected, is it the plug on the alternator or the battery wire on the back of the alternator? This will help in the diagnosis.
It sounds like the alternator field circuit is not turning off. This could be related to a possible malfunctioning ignition switch where voltage is still applied to the I circuit (light green wire with red wire tracer) with the key off.
A faulty voltage regulator could also be at fault where the charge rate is within charging specs but will not turn off the alternator field with the key off.
From what I understand is you are unplugging one alternator. If you have a duel alternator system the PCM could be causing the alternator field to stay on with the key off engine off.