Am I wrong or is ebay double charging its FVF??

The first FVF is suposed to be just for the selling price; check the math on yours.

Those transaction fees have nothing to do with the postage discount you get when printing your shipping labels through eBay/PayPal. If you want the shipping calculator to show the online rate (rather than the retail rate) you can choose that option in the shipping section of your Site Preferences.