After spending some time messing about I actually read the instructions. The new Swisscom TV 2.0 remote control is Bluetooth. Meaning your TV remote can't pair with the receiver and the Swisscom remote can't pair with the TV. If you want to use a multifunction/smart remote you'll need to by a Swisscom USB infrared receiver, around 25CHF. I don't know why Swisscom thinks this is a good idea, having to use two remotes (for now) is a bit annoying.
I think this post belongs here .
Can't say I've ever considerd it an issue, to be honest. I think it's quite nice you don't have to have LoS to the TV box to use it.
Well I posted it in TV/internet/telephone because that seemed the most appropriate being a TV related topic. This was not a post for me to whinge about the issue, I was merely bringing it to light to provide the information to anyone who may search this topic in future.
I bought the infra red doodah which works with my Harmony. I guess you don't use the optical jack which they also mucked about with. Keeps Swisscom in profit I guess.