I don't know if it'll work for you or not, but you might try this: Go into the 990's input menu when you have a DD or DTS disc playing and select "Dolby Digital" or "DTS" as the default mode for that input. "Stereo" as a default is going to be ignored since it doesn't directly relate to these modes.

I am guessing that you have a 7.1 setup, since that's the only way the PLIIx would be an option with a 5.1 source. If that's the case, is there a reason that you prefer straight DD 5.1 or DTS 5.1 to PLIIx (which still does the DD or DTS decoding but then uses PLIIx's matrix decoding to derive rear surrounds from the side surrounds)?