The little box is called the cross-over. Its what directs the musical traffic to the mid-bass and tweeter. its vital component.
If what a mid-bass and tweeter makes no difference, then you swap the speaker wires at the amp, from a channel that the speakers play normal over to a chnl thats not normal, whats the result, did the quite speakers play loud and the loud speakers now play soft? Or quite speakers still played quite after now being wired to what was a known good amp chnl?
RCA inputs can be an issue, The zone controller can be an issue. The amp can be an issue, or possibly an amp setting got bumped.
Michael
Mikes Liquid Audio