I have seen this answered a few times now on the forum and to give a simple answer - There is no real difference as both reflect the same thing. The reason why some states are different comes down to the GL of the state and an accident in history as to the office title for the state.
Here is a little something that sums it up perfectly --
"
It absolutely does NOT matter whether you join a F&AM or AF&AM lodge.
In the U.S.A. every regular lodge is under the jurisdiction of its state
Grand Lodge. There is no higher body than a state Grand Lodge -- no
Super Grand Lodge of the USA or anything like that.
Each Grand Lodge will be styled "F&AM" or "AF&AM" and all the lodges
under it will have the same initials as their Grand Lodge. But there
are no more differences between AF&AM bodies and F&AM ones than there
might be between two different states that were both F&AM. It's just an
accident of history whether a Grand Lodge has AF&AM or F&AM after its
name.
All Masons trace their "legendary" history back to the building of
Solomon's temple, with some old legends that even describe Biblical
story-characters such as Noah as Masons. But all Masons trace their
"operative" history only back to the mediaeval cathedral builders. And
we only trace our "official" history to the formation of the first Grand
Lodge in the world in London, in the year 1717."
Source :
http://web.mit.edu/dryfoo/www/Masonry/Questions/afam-vs-fam.html