Yes, it's definitely not in bypass mode when this happens, and it ONLY happens in 2 channel stereo mode...in anything else, the signal is sent properly. I also have my speakers set to small with the crossover at 80Hz. I don't have a crossover on my sub, so I guess I'll either have to change the 990 X-over, change the speakers to large or both if I want to listen to two channel...which isn't very often, so it's not ahuge deal...more of an observation.