I had a similar thing happen with my son's new SB1 5m.
Try leave the kite in the sun for a while to get the valve a bit supple, then manually ram the stopper ball into the neck of the valve stem using your hands, without any pressure in the bladder. Pop the ball out again and repeat a couple of times.
Then pump it up, hold the valve upside down and jiggle the ball into the seat before pulling out the pump nozzle.
I think in new kites the valve stems probably get out of "round" so the ball won't fit properly. Once it has been jammed in there a few times it gets the proper shape.
Technique works on a few other tight valves too, that we won't mention on a family friendly forum!