I know for a fact that its VERY easy to do a MD/masters in whatever at Duke because of the flexible 3rd year. I'm also sure that most medical schools will help you plan a 5 year curriculum for a MD/masters.
Stanford is definately leaning towards a 5 year medical program to make this possible with their "scholarly concentrations."
The new program at Cleveland Clinic Lerner College of Medicine is also specifically designed for people who want an MD/Masters as opposed to an MD/PhD and want exposure to research...
So in short, there are plenty of options available. Good luck!!