Pokemon obey you by what badges you have.
For a guide on which badges get you obidence from which levels, click: here
It doesn't matter if the Pokemon is traded or caught in game, if it's above a certain level and you don't have the correct badge, it won't obey you. You specifically need the Heat Badge in any Hoenn League for Level 50 Pokemon; you cannot substitute that badge for another for your Pokemon to obey you.
If you do have the correct badge, then your game is glitched due to your cheat.