The way the process for donating using Giving Works is set up, ebay/paypal gets to charge you money no matter what. I ended up losing money on a charity auction!
Rather than send the percentage donations to MissionFish directly, the money goes to your paypal account then you are billed by MissionFish. Even though ebay fees are pro-rated/waived for the donation percentage, they still charge the 2.9% paypal fee on the total amount!
This means that if you set up an auction to go 100% to charity, ebay/paypal still skims their 2.9% cut off the top!
I literally owed money to paypal after auctioning something 100% to a charity!