As this is very dependent on the Sky Box capabilities and settings I suggest you not use optical in this case.
The connection I use is HDMI from said box to the sound system and the sound system does the audio work and outputs the video on HDMI to the HDTV.
When folk run the optical like you noted, I find most bewildered at the settings that are required and then upset about lip or audio sync issues. Which is why I would never hook it up that way.
I have a Samsung TV and Blu ray Home Cinema System and Sky HD box. At the moment I have an Aux cable connected to the sky box from the Home cinema so i can get surround sound. I purchased an optical cable to connect my sky box to home cinema as the sound will be better but it doesnt work. I have the function for the BD on D IN. Anyone have any ideas. I have no issues when playing DVD/Bluray as this is connected with an HDMI cable. Hope you can help.