There was at least one generation of Yamaha receiver where the subwoofer output only had LFE signal, no matter what. You had to connect the sub using speaker wires, whether the sub had a high level crossover or not. Is it possible that this is the situation here?
A good answer is easier with a clear question giving the make and model of everything. "The biggest problem in communication is the illusion that it has taken place." -- G. “Bernie” Shaw