Did you change the name of the Skill entry that has the level as well? I think the game uses both to determine the penalty.

Code
new entry "Flying_Cows"
type "SkillData"
...


new entry "Flying_Cows_2"
type "SkillData"
using "Flying_Cows"
data "Level" "2"


If you wanted skill level 4-
Code
new entry "Flying_Cows"
type "SkillData"
...


new entry "Flying_Cows_4"
type "SkillData"
using "Flying_Cows"
data "Level" "4"