Since I built the thing ive been having this problem. I activate the water and nearly no seeds end up in my chests. I disabled the farm to not loose money. Maybe there are too many items on the floor at the same time. I have no idea. I would like this to be fixed. There are 600 dirt blocks on each three levels and 600 on the soul sand layer on top. Over 2400 crops at the same time, might be a problem. First pic is the farm. I even put hoppers on all layers to reduce item travel distance. The second is everything I got from a full harvest.