I certainly could be missing something, but it seems like everything is hooked up and set up properly. As you mentioned, your TV (as far as I can tell) doesn't have any menu settings for the audio output from the optical connection.
When using the Bypass sound mode, I don't think that you would be getting sound from the front three speakers unless the TV was sending a Dolby Digital bitstream to the receiver. If you were only hearing sound from the front two speakers, then I'd look into it further. As I mentioned initially, audio in the rear speakers is not always there, and when it is, is not typically very loud. It could be that your expectations for the rear audio are different than what exists in the TV shows that you're watching.
You could disconnect the front three speakers from the receiver unit and then have TV playing in the background while you do other things. If you ever hear any audio at all, then you know that it was from the rear channels. As a note, Dolby Digital does not mean 5.1. Not everyone realizes that. Dolby Digital is an encoding method, and it can carry up to 5.1 audio. My PBS stations are typically in stereo here (even though they are broadcast in Dolby Digital), and I own mono (1.0) Dolby Digital DVDs. That's just more info on why Dolby Digital broadcasts aren't necessarily going to have any audio in the rear channels (or even in the center channel).