We had a problem with our multiroom and it turned out because we were switcing the sky box off completely at the wall sky had switched our multiroom off - because they couldn't update the box and it's in your contract they be able to connect to your box whenever they need to ... failing that - we have had loads of problems on the sky hd box downstairs and there either being no signal or when we have something recording you can't get another channel.
Solved this the other day and it was the input2 cable at the back of the box - the end which screws onto the box - the male connector screws on and it seems it wasn't on right - completely removed it and put it back on, making sure the long thin wire which goes through the plug is longer than the plug - now it's working perfectly.
We considered using another box an this is easy as you only have to ring sky to pair up your card (free) - or investing in a second hand box and pairing that up - both alot cheaper than the sky options - the warranty offered by sky is £8.25 per month but I found out the other day that it covers all the boxes and remotes in the house - not just one box, but still think they're taking the hit n miss a bit due to the amount we pay £70 a month
we told them to shove multirom and HD before xmas but they offered us them half price ...so rude not to take it really - give them a call and they usually offer something to keep you.
Hope that helps .. failing that you can buy the double cable on ebay for the sky plus boxes