The good news - I have managed to solve the issue myself. Below is what worked for my problem, hopefully it will help someone else in the future.
After reading other people's similar problems and my understanding of my unique situation I was convinced the issue was software related and not with the equipment.
I made the mistake of contacting talktalk via phone and web chat to ask for advice. Their advice ranged from suggesting I needed to unscrew the box where my phone line enters the house to test the connections, the router / splitter/ youview box might all be faulty. I would need an engineer to visit to resolve the issue. All of these I was sceptical of.
Finally I decided to turn box off using both remote and also switch at back of box. Leave for a couple of minutes and turn back on. Go to check for software updates in settings menu, ran the software update that was now available and as if by magic the missing sky channels were now available to view live via the guide.
So simple, so quick but talk talk were unable to suggest this solution.
My advice - if you have a set up problem check with the community first, use your own common sense and only ask talk talk as a last resort.
