so you have all your pedals in a bypass loop, and even when they're all individually bypassed, there is a drop in signal when you switch in your loop?
Does it do this if you have your basses output turned down? Try about half way on the volume knob.
but yeh, you should probably solve the problem at the source, so go through each pedal and figure out which one(s) is cutting out your signal and maybe replace that with something better.