Assuming you are filling and draining through the same thru-hull fitting, you do not need a check valve installed when using an impeller pump (like your Jabsco). That style of pump will not allow water to flow through its manifold when it's not running, so it in turn acts as a check valve.
I would start by removing them from your system so you simplify everything. That will make tracking down the culprit easier.
Jason
www.wakemakers.com