I had that same problem with my 990 yesterday! I could control my TV with the remote but not the 990; even though the batteries were new I put fresh ones in and still had the same problem.
I then pulled the batteries out of the remote for about 15 minutes, put them back in and it worked like a charm! Give it a try, I also powered down the 990 and unplugged it for a few minutes but it did not start working again untill I pulled the remotes batteries and left them out for a while, not just a minute or two.
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Manley Stingray II
Merlin TSM-MMI w/Master RC
Sound Anchor 4-Post Mass-Loaded Stands
Eastern Electric Mini-Max DAC
Vortex Appliance
Squeezebox Touch w/Bolder digital mod & PS
Cardas Speaker/Interconnect Cables
Velodyne EQ-Max 10
65" Panasonic VT-30 ISF Calibrated
Outlaw 7700
Outlaw 990
Integra 80.2
Onix Ref 1.5 - Ref-100 w/Ninja Masters/NoRez
Oppo BDP-93
Hsu VTF-3 MKII RW
Furman Elite
BlueJean Cables