Wow! Just been reading this, and for my char's, they're always getting jumped, even at Morthal. And Alduin is dead as is Mirrak. Even battled them in Solitude. Only place they've not ambushed me is Markarth.
So, I guess they're all ticked at me or what, I dunno. But all 3 char's have a nice collection of Dragon Soul's.
Can't figure why they leave you alone, as I play on a 360 Black Box as well. Might be a number of thing's. it has kind of an AI in it I think, because stuff rarely happens twice in exactly the same sequence as before. I go back to places I've cleared, and end in fight's with Draug's and the Foresworn.