Oh no, that is terrible. I'm glad to have you as s new member,but sorry that such a dilemma has brought you here. I'm sorry your problems can be solved though, don't worry! ^_^
Will put this thread over in gaming instead of intros so that players or frlg and dppt will see it, and hopefully be able to help.
As djizzle pointed out though disobedience is associated with traded Pokemon being at a level higher than what the player can control at the gane stage. Gym badges are the proof of your advancement as a trainer, and by the time you collect them all Pokemon of any level will obey you. If they are Pokemon you captured in game it isn't necessary, you can grind to any level. But traded Pokemon are different.