If this has worked for you in the past something might be corrupted with the item in question.  What you might want to do if it happens again is double check the item setup and make sure that it only has the income account in the item setup.  If the setup is good, go back to the refund transaction and run a Transaction Journal report on it, this will display the debits and credits associated with the transaction.  Mainly you're just checking to see if the problem displays on that report as well.  If it does, then the item could be damaged possibly.  In that case to fix the problem (make a backup of the file first), you might want to recreate the item in the items list, then merge the original item into the newly created one.  After the merge you can rename it back to it's original name.  Then try the refunding again and see if that takes care your problem.  Merging an old item into a new item most times can correct a damaged list item.