Is it really? I'm curious why the original skills seem to be unaffected ... (or they seem to not be, at least).
They are affected, but the system come with default settings for them.
The "Tankentai Language" is quite complicated for non-programmers.
There's some tutorial made by Mr.Bubbles that might help you, check his signature (got lazy to search for the links), but that's all you will have.