I had the same problem plus the center channel. I tried turning the sub and center on in the menus, but it had no effect. I moved the microphone lower and re-ran the Setup routine. It found the sub and center the second time. I don't know if it was due to repositioning the mic or the 990 just missed it the first time, but all is well now. Perhaps that will help you.
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Outlaw 990
Outlaw 7125
B&W 703s, HTM7, DS7s, DS6s
Velodyne DPS 1200
Sony 60" LCD Grand Wega