VirgilRVA

I would imagine it's more likely to move from an MA in a related field to a PhD. What would your PhD be in? I know several people with underwhelming undergraduate histories who have gone that route with mixed success.
The biggest detriment to pursuing an MA outside of a PhD is the cost. But, because it sounds like you're going to utilize military money, that shouldn't be a problem. With regard to your question about admissions, having independent funding is definitely not going to hurt you.
My focus would be to make sure that there is somewhat of a linear trajectory from MA to PhD (ie: MA in international relations to political science PhD). When I think "professional-oriented" masters in this field, I tend to think MPA/MPP, which are not necessarily a great transfer to a political science PhD.

Well, I'll bite. It would help this discussion if you got some things out of the way, for the sake of honesty. Did you perform well at Fletcher? Would your professors speak well of you? Were any of the unpaid internships at prestigious organizations or agencies? Did you take any (Why not)? You only mention the State Department, what type of work were you expecting to walk into? What kind of money were you expecting to make and exactly how were you expecting your MA to impact your salary? How quickly are you expecting to get some of the higher paying jobs in the IR industry (intelligence, private intelligence, or various language related analytical work)?

Well, I'll bite. It would help this discussion if you got some things out of the way, for the sake of honesty. Did you perform well at Fletcher? Would your professors speak well of you? Were any of the unpaid internships at prestigious organizations or agencies? Did you take any (Why not)? You only mention the State Department, what type of work were you expecting to walk into? What kind of money were you expecting to make and exactly how were you expecting your MA to impact your salary? How quickly are you expecting to get some of the higher paying jobs in the IR industry (intelligence, private intelligence, or various language related analytical work)?