In d20, whether or not something is a class skill is determined class-by-class, so simply adding or removing it from the hero isn't going to do anything. (Unless, as you've seen, you use the "This is a Class Skill for all classes" mechanism).
The Animal and Knowledge domains add class skills to only the cleric class (yes, it looks like weather may be incorrectly applying it's effects to all classes).
Basically, you want to assign or delete ClassSkill.XXXXX from the class in question.
What is this on? A feat? A Class ability? Have you already figured out how you're selecting the class to target (or does this target a specific class)?
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