I think the issue is the settings in the S550. I had to track down the S550 manual, and I must say that those Sony boys are doing some weird stuff. Here's what I'd start out trying:

Audio Output Priority: Multichannel Analog
Speaker Settings: Front, Center, and Surround "Large", Surround Back "None" (950 only has a 5.1 analog input), and Subwoofer "Yes". Distance and Levels can be tweaked later.
Audio (HDMI): Auto (I'd prefer "off")
BD Audio Setting: Mix (otherwise secondary audio won't ever work)
Audio ATT: Off
Dolby Digital: Dolby Digital (why the default is "downmix PCM" I have no idea)
DTS: DTS (again, the downmix default makes me feel like I'm back in 1998 and DD/DTS decoders were actually rare)
48kHz/96kHz PCM: 48kHz/16bit is probably fine
Audio DRC: either Auto or Wide Range
Downmix: Dolby Surround is fine as a default, but we really don't want the player to be decoding multichannel and creating a downmix stereo signal so the hope is that this setting will be ignored.

Keep in mind that to use the 6CH input on the 950, you need to hit the "6CH" button on the remote - the DVD analog input is tied to the DVD input's stereo analog connection. The coaxial input can be associated with the DVD input normally, and you can use that for CD's, DVD's, and any Blu-ray discs you run across that don't have multichannel PCM, TrueHD, or DTS-HD tracks (there are some around - Planet Earth is an immediate example, but there are others).