The box for the main room has an IR emitter from a Nevo Link via a Nevo SL, and in the other room we're using the original Sky+ remote and a MagicEye.
So the Nevo emitter was sending commands to both boxes (not just the HD box), I didn't really want to cover up the sensor on the Sky HD box in case I ever wanted to use the original remote.
I found a site which has sorted me out - the bit that helped me was answered in Q3.
I just had to learn all the commands from the Sky remote again after I changed its settings.