This may or may not be anything to do with going via the Sky+box but I have noticed on many occasions both my Freeview boxes lose all the BBC channels periodically. Every other channel is tip top. It's like the Beeb have forgotten to feed their meter with 50p pieces. In the diagnostics menu, signal strength is still at the normal 35 or 36% but the signal quality has dropped from 98% to less than 20%, sometimes it is down to 0%
I have never seen this with any other Freeview channel.