That's an interesting question. I've heard of medical students transferring from one school to another all the time between second and third year, but never of an MD/PhD transferring. My guess is that the biggest roadblock is the funding issue. Many MD/PhD students are funded under institutional MSTP training grants, which are allocated to schools. So if one were to transfer to another MSTP program, they would have to be picked up on the grant at the new institution-- which is probably not eager to pick up a new student halfway through training (taking funds away from someone they could choose themselves).
I would think, though, if you are a real superstar and every program desperately wanted you when you were applying, *and* you had a good reason for wanting to transfer, you *might* be able to convince another school to take you on *and* continue your funding. Even so, I don't think I'd start at one program counting on transferring to another.