TommyBoy,
I use bypass mode for my CD player (non-SACD, Cal Audio Labs))because I don't want any processing by the 990. That's what bypass mode is for. Why are you using it?
My point is you should return your unit, because you are not happy with it. Life is too short for bad tone!
The 990 has a few quirks that I deal with. The sound for my HT is superlative, when properly set-up.
dave