When the self adjusting brakes were installed, you should always manually adjust them until they are set correctly. I see from your post you did that after the fact. Even so, they will have a break in period where your brakes will continue to self adjust, and the shoes will start seating with the drums.
As the new brakes continue to break in, you might have to frequently adjust your controller to get maximum braking efficiency. Take your trailer to a lightly travelled road or parking lot. Drive at about 15 mph. Using just the brake controller's hand knob, apply full braking power. You are looking for the wheels to lock up when the controller is fully applied. Keep repeating and adjusting until you get lock up. Once you get the brakes to lock up, back off on the controller setting. You should then be able to stop the trailer with just the hand controller and no lock up. I'd repeat the adjustment any time you notice diminished braking, and at 25 miles, 50 miles and 100 miles. After 100 miles, your brakes will most likely be seated and fully self adjusted. Of course, it's good practice to check and adjust your control settings on a routine basis any way.
