Hmm, it's odd how it ignores every Class Skill that was removed after the first one. It seems to just remove the first one for the Class Helper and leave the rest alone. Kind of odd. Anyhow, here is how you can fix this. Each class has a Class Helper, which has the driving tags for class creation, but the NotClassSk.? tags are being assigned only to the class variant (which tracks how many levels you have in that class, and a few minor things). You have to remove the tag from the Class Helper to get the desired result (you can ignore removing them via the editor interface, it just isn't working right). I've run into a few of these tags that aren't working, and have had to remove them myself (alignment requirements is one, but I digress). Use this code in your class variant, where the Class Helper is for the class you want to modify.
@First/5000
Code:
perform hero.child[cHelpXXX].delete[ClassSkill.kXXX]
So to remove Decipher Script from a Wizard, you would add this to the class variant scripts:
Code:
perform hero.child[cHelpWiz].delete[ClassSkill.kDecScript]