almost forgot to obvious are you sure you didn't set the ailerons up with the flaps switch in the wrong position that will give the throws your talking about and still let the flaps work also don't forget about the flap rocker switch be sure it's center along with trim and sub trim and servo travel is equal in both directions
it's best to take your linkage off before you mess with it so your don't jam a flight control and strip your servos after you do that check the servo arm travel with both positions of the flap switch I'll bet you have it in the wrong position in the flap up position the arm will move equal in both directions in the down position it will move more in one direction and less in the other like yours is doing