Quite simply because Sky have absolutely nothing to do with BBC HD. It's encoded and uplinked to the centre by Red Bee Media out of TV Centre. Literally the only thing Sky do with regard to the BBC channels is insert them into the EPG.
I was getting it too but got relegated upstairs for the second half and it was the same on BBC1 on SD Sky. Must have been a problem with the feed from the ground, although that would n't explain why it was doing it in Hotel Babylon.