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There's three fields you might be adding to, but you don't provide enough description of exactly how the rules of your trait are phrased that I can tell which is the right one.
The skInnate field is for pre-assigned ranks, like the ranks assigned to an NPC, and the skExtRanks field is for ranks coming from external sources, like the effective ranks in skills granted by a bard's versatile performance abilities or the effective ranks a familiar gains in the skills their master is trained in. The skItem field is for ranks granted by a magic item, like a headband of versatile intelligence.
The question is - how do you want these free ranks to stack with ranks added by the user? So if a character has a few levels, and then uses the Additional Traits feat to buy this trait, what if they choose a skill that already has some ranks in it? Do you just want to grant enough free ranks to = their current level, or do you want the existing ranks to become an error, so that the user is prompted to retrain the existing ranks and spend them on other skills?
Also, your original post left out a very critical piece of information - the phase and priority you've assigned to your script. Without knowing that, I can't tell if you've made a mistake in timing, and that's what's causing the trouble.
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