I was trying to check the URL provided, but I'm getting a '503 service unavailable' error at the moment.
I might have an idea though. Are the products marked with the parent categories as well, or only with the sub-categories?
If only the sub-categories, then it explains it, as in that case there is no direct connection between the unchecked term and the product. Let me know if this is the case, I might be able to construct a custom code solution to exclude the parent categories as well.
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