I had exactly the same thing happen to me, but I had bought two items from the person and he only shipped one, so I had to get a refund. Now the problem was that the way Paypal works it will not accept a partial refund, it is either gets a full refund or nothing at all. Fine so the seller then sent me the money as a payment, well paypall then proceeded to take 3% out of that payment, at which time I had to spend almost two days on the phone to get it straightened out, which eventually they did. Bottom line is look for the refund check that it is all there and if it is not argue like hell and do not give up, eventually they will relent.
On a side note but in the same general area, lately I have seen several people charging paypal fees on transactions here at the 4% level, in effect making a little extra money on the side if the sale which irks me to no end. It is not a matter od the extra 1% but the fact that they are trying to convince people that is the correct fee like most of us are not up on this.