Check the alignment of your storage box - the seal needs to be engaged correctly to seal out the water. If it is loose or misaligned, the weight of the hatch when rolled will pull away from the rest of the hull and possibly let in water.
The big thing is if your boat can evacuate the water quickly - either by the stock venturi pickups or an aftermarket bilge pump. That way the water is removed without a cumulative effect of what could end up being a VERY full hull of water.
Might want to check out the carbon ring at the rear where the shaft enters the hull (on the inside of the hull). It should not be allowing water in while running or at rest.