I think the percentage is 3.9%. Payment Proccessing fee is payment for processing the payment, whether for 5 items or 1 item. Transaction Fee would be for each transaction, so probably per item.
Etsy's processing fee is 3% of the total transaction - sale of the item AND shipping fees + $.25; the transaction fee (I believe) is the same thing, just different wording. The listing fee of $.20 is to list an item before it is sold.