Maybe try restting the unit to see if that helps. I've run the auto setup routine a couple of times. Every time I've run it it hits my sub with double the tones of the other channels but shorter bursts. Not sure if that's normal either. Seems to work OK though.
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Marantz av7005 Proc.
Oppo BDP-83
Rotel RB-991 (mains)
Outlaw Audio Model 2200 (center)
Rotel RMB-1075 (ss, rs)
f, B&W DM604S3
c, B&W LCR600S3
ss, B&W DM302
rs,Polk M3II
HSU VTF-3 MK3
APC H-15 Power Conditioner
Display: Panny PT-AE4000 Proj. + 92" DIY Screen
Little Dot MKIII Headphone Amp
Denon AH-D1100 Headphones (needed a quick, cheap set. looking for an upgrade worthy of the h/p amp.)