I have just recently experienced the same problem: PayPal is deducting the cost of shipments for my sales on ebay from my PayPal account--but then they are also charging the "backup funding source," my bank account (which is on a thin margin because I'm disabled and has resulted in multiple overdrafts.) So now I have two fights on my hand: Persuade the bank to overturn the overdrafts, and figure out what on earth is going on with PayPal double charging customers on shipping. I also am unable to find any options in either PayPal or ebay on preferences for payments on shipping. I have always listed PayPal as my first shipping payment option and always have enough there to cover those. There's no excuse for double charges.
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