Something could have been pinched. I recall reading where the fittings can go bad b/c there is no wiggle room for the hoses when they fill. If that model has the faux back wall on the transom, I would take that off and start there. It should only be held in by ss screws.

Per the stacking of the bags, have you considered upgrading the bags to appx 1200#s (I think the ballast bag companies they make 1150# or 1180# bags)?
One bag vs Two - then adjust the fill times?