The problem became apparent a few months ago when I woke up early and started the box while it was in it's power saving sleep mode. After powering up the remote didn't work. I then power cycled it over and over again until by magic the box started to obey the remote. All the advice on the BT site (like resetting the remote or the box) didn't work.
So, when this happened to me again this morning, I tried a few things (like switching off the TV whilst power cycling). However what I found to work was to do the following:
THE SOLUTION WAS TO POWER UP THE YOUVIEW WITHOUT THE ETHERNET CABLE CONNECTED.
You will find the remote is working but that all Apps are disabled. However, you can then plug in the ethernet and the apps will all jump back to life after a few moments, and the remote keeps working.
I must admit I didn't repeat the problem to check that this is definitely the answer and not just a fluke... but I will update this if in future I (or someone out there) find that this fix doesn't work.
I suspect that when some of the apps start up and do things over the internet, they cause something to get screwed/delayed so that the YouView software fails to startup the remote (and sometimes the box top buttons) interface software.
Hope that helps folks!