@carlskie
What i always do before activating the perk option is to legit get one or two perk points which is easily doable by finding a deer or pronghorn in the wild or fishing any kind of fish. After that, i get the game tutorial on perks, close the menu (without spending any perks ofc), activate perk option in trainer, open perk menu tab and spend all of it. I only use it once cuz 99 is enough to get all of the "must have" perks based on my playstyle. It always works for me. I had trouble at first when i used the perk options BEFORE getting the game perk tutorial (when you first legit gain a perk point), ever since i started using the perk option AFTER getting this tutorial, the issue never reappeared.