We ran into something similar a few weeks ago.
We tried to issue a partial refund for the overpayment of shipping, and were faced with an "ALL OR NOTHING" proposition.
We believe it has to do with the fact that the buyer has used some type of promotional offer.
It was nothing more than a $3 overpayment, and was unrelated to any claim, or other issue. The buyer simply multiplied FOUR items- at a buck each, not realizing that we provide COMBINED shipping for US$1.oo.