Ok I've got an interesting one here.
This is the Denon AVR-1603 with 80Hz crossover

Red = V.AUX input and CDR output
Purple = EXT. input and SUB output
Green = V.AUX input and SUB output with speakers set to LARGE(LFE+MAIN on/pff didn't make any difference) set to both STEREO/DIRECT(this trace is also the same with speakers set to SMALL but with prologic cinema or DIRECT enguaged)
Blue = V.AUX input and SUB output with speakers set to SMALL set to STEREO
Something really screwy going on there

I even reset the microprocessor but it didn't make any difference.
Any ideas?
cheers
