I had a similar problem happen to me last night. I've been using Paypal now for about 10 years and have always used my Visa credit card as the primary funding source for payments. However, after making a purchase on Ebay on 03/15/2011, I noticed that Paypal deducted funds directly from my checking acount. I telephoned their customer service line an spoke with two agents: Gale and Kathy. Both gave me the run-around and told me that while their system did allow for my account to use my checking account as the primary form of payment, that there was nothing that could be done to reverse or stop the payment. Ironically, they both told me that this "feature" was an added benefit of Paypal for customers in good standing. While I consider myself a lucky one because I had enough funds to cover this payment, I could have easily become one of the many that do not have enough funds and then face hefty over draft fees. If this happens to you, I suggest you do two things; 1) Contact your state consumer frauds division, and 2) File a complaint with the Better Business Bureau (http://www.bbb.org/us/find-a-bbb/).
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