The issue regarding Top Rated Seller discounts not being shown on invoices has been resolved. All affected sellers have been contacted by eBay.
For impacted sellers, the accurate amount - including the Top Rated Seller discount - will be processed via the payment method on file, and resulting net charges can be seen on My eBay and Seller Hub.
We know this is a busy time of year for your business, and we apologize for the inconvenience. Thank you for selling on eBay, and have a safe, happy, and successful holiday selling season.