I've got the same issue. The 990 seems to default to Stereo regardless of the audio input setup for CD playback. I've set the "Surr Mode" to Bypass and audio to Analog in the audio input setup for CD playback and if you turn everything off or switch to 7.1 audio the 990 reverts to Stereo for the Surr Mode setting when you go back to CD playback's audio setup page. I've not found a solution and it is an annoying hiccup since I want to use the Oppo's audio section. And I imagine with the SE version you'd really want to take advantage of its upgraded audio capabilities.
FYI, I've not found an issue with the video input setup for CD playback where I use the coax output from the Oppo and leave the 990's Surr Mode set to Upsample and it retains that setting.
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AvFan
Outlaw 976 | ATI 2005 | M&K 850s Left, Center & Right, Surround-55s, MX-70B Sub | Harmony 950 remote | Panamax 5100 | OPPO UDP-203 | LG OLED55B7