Overall, I'm please with the Oppo, but the 990 is getting me a bit irritated now because of this. So to sum it it, I have to do "work" depending on which source I want to use:
1) For HDTV (optical) from cable box, have the 990 set on "small" for all speakers with it using its internal bass crossover.
2) For DVD/BD playback through the 7.1 Analog input, change all the speakers size to Large on the 990, which will bypass its A/D/A bass crossovers, since the crossovers are already set on the Oppo.
3) For CD playback through the 7.1 Analog input, speaker size set to Large on the 990 (as in #2), but turn off the surround speakers by selecting "none" to stop the white-noise.

The only way around #3 is to connect the 2ch Stereo RCAs from the Oppo to the CD Analog input on the 990. That way the 990 won't send any signal to the center and surround speakers, eliminating the white-noise sound from those. But in doing this setup, having the mode set to "Bypass", and the front left and right speakers set to "Large", the Sub will not be in use. I'd have to set the front speakers to "small" on the 990, which then introduces the A/D/A that I wanted to avoid.

Hmmmm!