So? Are you using switched 12 volt power originating from the bulkhead to the ballast as your source of 12 volt power? If so? That`s bad. The VR is seeing the swing in voltage thru the bulkhead and is over reacting to it.
You need to run the ignition and the voltage regulator from a key switched "relay" that is being supplied with clean 12 volt power straight from the battery. You can use the wire that goes to the ballast as the trigger for your relay. I did this to my Coronet and all my weird charging issues went away and the ignition system loves good stable voltage.