This is your problem - you have no video connection between the 990 and the TV. As a result, there is no way for the 990's setup menu to be displayed on the TV. You need to run at least a composite or s-video cable from the 990's monitor output to the TV and use that input while setting the 990 up.
The 990's menu is available over component (it is mine anyway). It shows up over whatever is playing (i.e. DVD, TV, etc.).
Rick
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Outlaw Audio 990
Outlaw Audio 7700
OPPO BDP-83SE
Playstaion 3
Panamax M5400-PM
Sony VPL-VW60
Stewart110" FireHawk G3
North Creek Music Systems CM-7's
Dayton Titanic 15" MKIII subs (2)