The 990's bass management is tricky. First question, what firmware version are you using? I had trouble with my sub bottoming out after I upgraded to the latest 3.11. This weekend I went over my channel settings with an SPL meter and the sub was too high. I turned it down 5db and now the whole system sounds better. Also, I don't know if you're handy with wood at all, but I highly recommend any of these "tuba" subs. http://www.billfitzmaurice.com/index.html I have the Tuba 18 and it fills my 11x25 basement no problem.
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Outlaw 990
Epson 750HD
Dish Hopper/Joey
Oppo 980 + Panasonic Blu Ray
2 Adcom 5400s + Adcom 6000
B&W P4 Front
JBL studio s center
MTX surrounds
"Tuba 18" sub