By any chance, do you have the universal player also hooked up via L/R analog connections? For that input (DVD, Video 1, whatever your universal is using as its input to the 990) how are you selecting your audio input in the setup menu of the 990 (in the on screen display).

If you're connected with both digital and analog connections from your universal player, but you have "analog" as your input type selected in the 990's OSD, all will seem to work, but you will get the result you are getting. This is the case that gonk suggested -- being connected to the 990 via analog.