Most programs would not encourage this, from what I've heard. It's less rare to make the MD-to-MSTP jump; that depends somewhat on the program you'd be talking about.
As for your "schools that are really good in what I want to do my future research in"... One of the joys of (most) MSTP programs is that you don't have to choose an area. And in fact, I think most MSTP students should instead choose a <i>mentor</i> and his/her lab rather than a department. Find someone whose philosophy really agrees with yours, and who understands and supports your goals (whatever they are). That'll matter much more than what department they're in.
Besides, most MD/PhDs that I know take their independent research programs in a totally different direction than they were working on as graduate students, since most basic science labs are pretty separate from clinical departments, whereas many MD/PhDs end up in clinical departments, with their research aligned accordingly.
My advice (worth what you paid for it, of course): Find out if there are good people at the MSTPs you got into that you'd like to work with, regardless of their research area. If there are, and you're committed to the MD/PhD idea, then do that. If you're not totally committed to the MD/PhD, then for goodness' sake, <i>don't do it</i>! Go to one of the PhD programs and forget about the MD.
