Absolutely, and this is precisely what I'm doing now with the support of my graduate department/advisor and while also being overseen by the med school. I'm scheduled to take ALL the courses required for the PhD and a few for the MD ( 1 down, 3 to go) and I plan to finish the Masters in the Spring of 2008 after having also passed my written exams for the PhD. Depending on how soon I find a lab, I plan to also have my oral exams succesfully passed and if things go as well, I'll only need to complete my dissertation research after Spring 2008. My plan is to start the MD/PhD program in Summer 2008 needing ONLY to compete my dissertation research and defend it.
Of course, my acceptance to the MD/PhD program will depend in large part on how I do on the MCAT in April and in my classes. If for some reason I'm not admitted to the MD/PhD program for Fall 2008, I plan to matriculate into my school's 5 year MD program and formally enter the MD/PhD in 2009. And yes, ALL my classes will count toward both degress should I be admitted.
Bottom line, there's more than one way to skin a cat, find what works for you, sell a school on your plan, then WORK the plan!
Good luck!🙂