Well, for one thing, the Warner HD-DVD's are improperly mastered on the audio side - I've seen several reviews warning that the audio is at significantly lower levels than DVD's or Universal HD-DVD's.

Technically, 0dB on the 990 is reference level - that's the level that folks calibrate it to in order to achieve the same volume level used when the soundtracks were originally mixed. Reference level is generally very loud, which makes me suspect you're not quite getting to true reference level at 0dB. What are the channel calibration settings produced by the auto calibration? Are they near 0dB (plus or minus a few dB), or are they consistently negative values across the board? While I'm rattling off questions, do you have an SPL meter so that you can manually run some test tones and determine what levels you are getting? Also, how big is your room?