Kugumby raises a good point, and one that can easily be checked with the 990's front panel display.

Your comments suggested to me that you had bitstream output correctly enabled on the tuner (it should be the default for an HD tuner) and you were just running into a lot of Dolby Digital 2.0 content. To be sure that is the case, check to make sure the "PCM" indicator (immediately to the left of the "Dolby Digital" indicator on the 990's front panel) is not lit up while you are watching over-the-air HD. If it is not, then you are getting the Dolby Digital bitstream that you ought to be getting. If it is, then you need to poke around a bit in your HD tuner settings.