I have within the last week swapped back to Virgin from SKY and to be honest, not sure I'm happy.
I have 2 V6 boxes and one works perfectly well and the other suffers remote control issues. I have changed batteries, reset the V6 box many times, and continually re-paired the remote (when it connects).
I have been told by the customer service team that it's a common issue and have to keep resetting my V6 box until resolved.
Try explaining to a 7 year old why she can't watch her TV!
phone and select thinking to leave (or whatever it is these days), you should still just be in your 14 day cooling off period.
Not being able to control one of your boxes is not acceptable so you need to talk to someone competent.
As an aside you could reset your remote and just use it in IR mode instead of RF, lot less responsive though.
p.s. I assume the upstairs remote being able to control both boxes depends on which one it is paired to at the time.. in RF mode it should only be paired with one box and ought to only control both boxes if in IR mode.