Ballast Issues - Jabsco Ballast Pupppies

Just finished installing a ballast system using 2 Jabsco Ballast Puppies. One pump fills the side bags and the other fills the front bag in the ski locker and a bag under the rear seat. The front and rear bags are vented, as I can't easily see them however the side sacks are not as they are on the floor. The pumps are mounted horizontally in the rear of the boat and the thru hull fitting is on the transom (one for each pump). I am having an issue with the front and rear bag empting when we are wakeboarding. How is this possible? Is there somehow that the flow of the water on the transom creates a vacuum or moves the impeller to empty the bags? If so how can I stop this? There is not really any room for a ball valve between the pump and the thru hull fitting however I can fit one before the bags, or should I use an electric gate valve? Is it essential to have the shut off between the pump and the thru hall or as long as it is before the bags will it be ok? Does Jabsco specify if their pumps should be mounted horizontal or vertically and would this cause the problem? If I require a valve due to accessibility issues, the gate valve would be my best option but I would like to know on this type of system is a valve required or normally used? Any help on what kind of gate valve would be appreciated.