I think I can help you, I am an officer in my med school's chapter of AMSA. The organization began a long time ago as the Medical Student Branch of the American Medical Association (AMA). At that point it was called SAMA. However, the students realized that they needed to be an autonomous organization in order to do the kind of things that mattered to them. The AMA was disinterested with their concerns (things like hours worked by residents, making the match favor students not programs, etc).
So the group broke away from the AMA, and became AMSA, the American Medical Student Association. So yes, the AMA-MSS is a completely separate group. AMSA today has over 30,000 members, and is completely student run. Also, in case you're interested, there are undergrad chapters of AMSA for premeds. I don't believe the members can become national officers, but I think you can get involved with one of the 8 committees. I hope that helps.
Mango