When you view an individual order that was paid through Paypal, the invoice shows you the total, the paypal fee, and then the new total minus the fees.
However, the reports do NOT include the fees in the total. The Gross value is correct, but the Net value that takes the shipping and taxes into account should also show the paypal fees, or even a total fees section on the left where the "refund amounts" etc. are.
It makes calculating how much we actually took in troublesome as we have to manually calculate the amount after fees by looking and adding up through Paypal's Activity After Fees section in a spreadsheet.