I have exactly the same problem with my Samsung LCD TV and with my Samsung Hard-disk recorder. For some reason, when you turn on whichever is connected to the Virgin box, the Virgin box stops responding to the remote control for 15 minutes or so. You can tell this because the little light doesn't come on the virgin box when you press a remote key.
I've never found anyone to admit that there is a problem, but I'm guessing that there is some sort of conversation going on between the Virgin box and the TV through the SCART cable.
It didn't do it with my old plasma or DVD player.
I just tune in the Virgin box before I turn the TV on - or turn the TV on 15 minutes before i want to watch it :-(