I've had great luck with the FC both threads down (my carved German factory bass) and threads up (the only way it will fit the bridge on my Kay). There's an outside chance that you just have a bad pickup from the factory. Anything that's mass produced will have some unit-to-unit variability and although in my experience Fishman seems to have pretty good quality control, I really doubt they install every unit on a bass and check out how it sounds before it leaves the factory. They no doubt have functional electrical tests, but that might not show the problem. So, if you're absolutely convinced that your bass has mostly even response across the strings (with the new bridge - that's the other independent variable and confounds the problem somewhat) go back to wherever you got the FC and ask for a different one. If it still sounds the same, you've eliminated one variable and now you can start trouble-shooting the new bridge and then maybe the bass itself.
Mark
Mark