How do I prevent objects/text from changing color when changing layout? - powerpoint

I have a PowerPoint template with a number of custom layouts. The template has a custom color palette, and layouts are organized under multiple Slide Masters that each use one of the color in the palette. So layouts are the same for each Slide Master, but feature a different color. All Slide Master use the same custom color palette, which has Black set for the Dark 1 color, and White set for Light 1.
The problem I have is when I create slides from these layouts, some end up with White as the first (Dark 1) color, and Black as the second (Light 1) color on the palette, while others have it the other way around (Black then White for Dark 1 and Light 1), as I would expect. This means that if I change the layout of a slide, any object that was white becomes black, and vice-versa.
Why does that happen?
I have tried re-selecting the color palette for the problematic slides, but it didn't help. I don't know what else I can try.
Any help is very much appreciated :)
Vincent

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