It's probably the dual winding on the cutout relay that's different. The direction it's wound around the armature would have an effect on how well it neutralizes the magnetic field when the reverse current happens on shutdown. That's critical, as an opposing field must be created to allow the cutout relay point spring to snap the contacts apart at the instant the fields cancel each other out. Otherwise, the reverse current holds the points shut, and allows the field to re-establish itself and discharge the battery through the stuck points.
Sounds sort of like your situation, doesn't it? We dealt with those problems quite often back when DC charging systems were almost all generator-equipped, before alternators became popular. I don't expect to change your mind about what's happening- - - -I've pretty much given up on ever doing that- - - -just relating what we dealt with back when the family shop was the most respected automotive electrical place in Nashville.
Jerry
