EDIT:
Okay, figured it out! Finally! I was looking in the engine .bin's, assuming something was pointing to the wrong fitting folder. Wrong...
Actually, each .bin file in the fittings folder for each repaint has to be edited to point to itself (point to the non default fittings folder).
Wow...I'm starting to see why its set up this way for the purpose of repaint flexibility, but this is pretty complex.
Ok. Crisis over, back at it.