*edit* I had mixed up the issue you are asking about with a different issue that someone is having... please disregard my previous reply...
If you are on managed payments now, there is no more payment processing percentage charged (yay ebay!)
They only charge a flat payment processing fee of $0.30
We havent set up that charge to come through yet but we will as soon as possible.
In the mean-time, you can type in 0.30 for accuracy.