Okay...so optical is outputting audio but you just can't adjust it via XR11. Nuts! With the TV configured for external speakers, I wanted to test if the codes (XR11) could still instruct the amount of volume from the TV. I guess not. In optical mode, the TV is only sending un-amped, audio data. Meaning, it's just data bypassing the TV amplifier. Is there an optical connector on your Contour Box?
Moreover, an optical cable/connector/port only supports audio data. Meaning, via optical, there is no 2-way communications between the TV and SB; therefore, the SB can't send its make & model numbers. I guess you could think of optical as only passive, 1-way data. HDMI, on the other hand, is 2-way...negotiation...syn/ack. We just need to figure its lack of audio.
Have you disconnected the optical and analog cables to test HDMI?
I'd turn off AnyNET to test HDMI. Sometimes CEC creates more problems than it's worth.
However, as a complete stab in the dark with AnyNET, is your SB listed in the AnyNET Device List? If so, any audio options?
Ensure the version of your HDMI cable matches at least the HDMI version of the TV. Since the SB is newer, I'll assume it has a later version of HDMI.
I read the manual for your TV and this doesn't look too promising.
Page 11: "When an audio amplifier is connected to the AUDIO OUT jacks: Decrease the volume of the TV and adjust the volume level with the amplifier's volume control." (Meaning, powered speakers, such as your SB, are technically an amp. The SB is an amplifier but with built-in speakers.)
Page 20: "When Speaker Select is set to External Speaker, the volume and MUTE buttons will not operate and the sound settings will be limited." (Meaning, although the XR11 or TV remote is sending volume control, the TV is ignoring the IR commands.)
Page 42 (Troubleshooting for Anynet+): "If your receiver supports audio only, it may not appear in the device list."
Workarounds? I don't know. With HDMI and optical, the TV is pretty much "hands off" with audio. An audio connector on Contour would help.
Disable Anynet?
An A/V receiver would work but if your SB only outputs 2-channel stereo, what's the sense? However, the sub would engage.
Since Contour doesn't recognize Pheanoo, you're limited to optical and the Pheanoo remote.
A learning remote would work but as you wrote, no RF.
A Universal Remote Control app on a mobile device could work. You'd just need to find a device with both IR and RF blasters. Then again, could this app control Contour? Also, from my experience, apps performing even the simplest tasks are annoyingly slow. First you'd need to wake the device, launch the app, navigate the app, re-establish the connection and have the app convert your commands into signals...and I'm sure the RF signals would travel on the already-congested 2.4 GHz frequency. If you have an Android device with built-in blasters, it'd be faster. Non-blaster devices would be slower.
There isn't much audio troubleshooting in the manual but I'm sure you've already scoured it.
www.samsung.com/.../