Hi Mark76,
The "Final Value Fees" section of a given payout report should typically populate automatically within about 4-6 hours of when the listing ends. However, the "Paypal Fee" field cannot be populated automatically because that information is not available through the eBay/Paypal API.
If you find that the "Final Value Fee" fields of your payout reports are not populating automatically as I have described above, please file a support request using the appropriate link on our help page: http://www.auctiva.com/free-auction-software-help/help.aspx
-Mike