If I am not wrong the handling fees have to be incorporated in the shipping charges, at least that's how I read the rules.
If the fee is charged after may be you should open a dispute and see what eBay thinks of it.
My last time I had an argument was because an overcharge shipping. The listing had fixed shipping fee but the postage was 3 times cheaper, the seller told me the difference was for his time and gas to get to the PO. eBay decided that was Ok. I feel that all fees should be incorporated in the shipping fee listed, and also explained in the listing. In my case I am not sure why one would charge for their time when they are willingly selling items, no one makes them to do it.