eBay sellers who have to refund buyers are finding a glitch that appears to prevent them from recouping related fees. However, there may be a workaround solution.
Typically sellers who need to issue a full or partial refund for a transaction click a link at the bottom of the transaction page that takes them directly to the process refund page. Refunds automatically appear as part of the original transaction when the link is used so that the seller receives a partial refund of fees.

The link now tells sellers to issue refunds through the Send Money link. However, when sellers use the Send Money tab, the refund is deducted in full from the seller's account, and the seller receives no credit for fees on the refund amount.
Sellers on a discussion board pointed to another link on the page that does appear to work, see this discussion board for more information.
The problem has been occurring since at least Sunday. AuctionBytes has an inquiry in to PayPal's PR department about the instructions to use Send Money.