In Pokesav under the input ID in the pokemon creator is an input for Secret ID this is the value that determines if a pokemon is truly yours or not. Pokesav has this weird habit of changing your Secret ID to 65535 so on the main page of Pokesav just change your Secret ID to 65535 and your pokemon should listen to you. Here try that
I was wondering in the Pokemon challenge - when I ever I use pokesav to put in a new pokemon the game treats it as a traded pokemon (It wont obey after a certian level :() what can I do to fix this?