Did you install the FMU from Paxton? It looks like a flying saucer and has two fuel lines going to it and a vacuum line. The FMU diverts excess pressure back to the tank if you're not under boost. It receives a boost signal from a vacuum/boost reference such as the vacuum line attached to the brake booster. The boost pressure overrides the internal spring and allows higher pressure to reach the fuel rails and hence the injectors. Without boost the spring prevents excess pressure from reaching the rails by diverting fuel to the return line to the tank. The springs can be changed to alter the point where higher pressure reaches the injectors.
I've always been under the impression that it didn't matter so much what the pressure was before the FMU since it won't reach the injectors. I used to have a 65 Mustang with a Paxton and a Weldon pump capable of putting out well over 100 psi. The fuel pressure as measured at the rails was 40 or so until we went to boost, then the FMU allowed higher pressure through. The pump provided a constant pressure regardless of boost level.
Bottom line, IMO, you do not have the FMU connected properly or the internal spring is wrong for your application. It is true that the Split Second controller is set up to turn on the two auxiliary pumps at different boost levels but my guess is that this is so they aren't running unnecessarily when they are not needed. I'm not an expert but I believe I could turn both pumps on all the time in my 06 supercharged FE Coupe and not have an issue.
Good luck.
