Actually, Plantinga is not making an inference to the best explanation here.  Rather he is claiming that one cannot be rational while accepting both naturalism (construed by him as physicalism) and evolution, because evolution gives the naturalist a "defeater" for the belief that one's cognitive faculties are reliable.

He argues by analogy.  For instance, suppose we learn of an extraordinary poison which usually (but not always) causes people to become almost completely irrational, so much that they can't even understand that their thinking is impaired.  Suppose further that we learn we have imbibed this poison ourselves.  This gives us, Plantinga argues, a defeater for R (the proposition that one's own cognitive faculties are reliable).  By analogy, the combination of E&N (evolution and naturalism) likewise gives a person a defeater for R.

(Please note that I cannot recall whether this PARTICULAR analogy is Plantinga's or one of his disciple's.  But either way, the point is the same.)

Personally, it seems to me that the analogy is flawed in at least two serious ways.  First, the poison is not comparable to evolution, because it is not true that we should expect evolution to result in unreliable cognitive faculties.  This is the tack that most critics seem to take to Plantinga's argument, and it is a good one.

However there is a second (and in my opinion more assured) reason, often overlooked, to reject Plantinga's argument:  Drinking the poison does not in fact give me a defeater for R, as long as the qualification remains that the poison does not always cause R to become false.  The same goes for other, similar analogies.  As long as it is our own cognitive faculties in question, we must trust them.  It doesn't appear to me that I have any choice in the matter.  In other words, we must take it as a basic assumption that R is true.

Now, turning finally to emailestthoume's question, I don't see any circularity in Plantinga's argument of the sort described.  It is true that we start off believing R.  Plantinga's argument presupposes R in that sense.  But with R in hand, Plantinga tries to show that the conjunction E&N gives a person a defeater for R.  Thus one is led (so Plantinga argues) inexorably to irrationality.  If he rejects R, then he cannot rationally believe anything, but if he accepts R, then he is led to reject R, a contradiction.  Either way the evolutionary naturalist is (so Plantinga argues) irrational.