You will certainly take it to your dealer for warranty repair to solve this issue.
I will tell you my recent experience with taking my Flo-Rite valve apart after purchasing a “rebuild kit”. Our Bass Boat configuration uses a V2 valve that has internal flappers in the 4 and 6 position on a rotating cylinder. Mine had 3 flappers and the rotator was installed 180 degrees out of phase. The result was that my valve worked in auto and empty but it would allow water to enter the live well in the empty position. I fixed it myself but I keep hearing of problems with the valves so I think it could be a Flo-Rite factory problem where training and experience is lacking.
This may sound crazy, but you need to check your “flush valves” first and make sure they are in the Closed position. Some people have reported this as their problem. At any rate, take it to your dealer for warranty troubleshooting and repair after checking the flush valves.