Ok, so the verdict is that some programs have Dolby Digital but it's not the default audio stream. It turns out my TV (Philips) is doing the down-mixing to stereo. Apparently the HDCP part of HDMI forbids audio pass-through to SPDIF. (That's a fail, really.) Apparently some Philips sets (xxPFL9603/9703) used to unofficially allow it on their HDMI3 input but subsequent firmware updates removed this "feature".
On the video format topic, I agree it's a huge pity the Cisco won't simply use the program format. Especially since it varies per channel, and in my testing so far my TV upscaler is significantly better than the Cisco one.
Even if it did this, there should never be a risk of the Cisco switching to a format not supported by the TV: HDMI allows the Cisco to enquire about supported formats. (Sensible behaviour when the TV doesn't support the current broadcast behavior is debatable, but not terribly complicated.)
As a workaround, discrete IR codes for switching the video format would be most welcome. I probably wouldn't mind the lack of an "original" option if it wasn't such a pain to change via the menus.