The whole bit about the confusing Cally escape scenese have me really worrying that she's a Cylon (which wouldn't make sense...right? Unless she killed Sharon in S2 to keep her from talking or being tested or whatever, all pure assumption). Like, they're might have been 2 cally's in the transport, as the one in Ep1 falls down the hill and into the forrest, and the one in Ep 2 was entirely different, like she came from the backside of the convoy, running away from the cylons.
Maybe it's a new thing they've developt, a way to simulate an actual person, so one is real and one is not. Maybe the fake one was meant to escape while the others died to infiltrate the Chief's group ("I got away before they all got shot, help me. Don't look behind me, it's a bomb!), only to be foiled because the actual Cally got away.
I made all that up from guesses, off of how the difference in scenes was presented to me. Because that shit made no sense to me at all, really fubar'ed