Addition of Self Illumation Map is Breaking the Base Map Paint Mask

I have an item with a paint mask base alpha that works just fine, but when I import the self illumination map it acts as if it's blending the tint without a mask. The whole item takes on the tint. The illumination map acts as it should, though. When I disable the illumination map the base alpha acts as a tint mask, as it should. This happens regardless of the phong mask.
Also, is it possible to link the illumination tint to the paint tint? Does it do that regularly?
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