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I'm experiencing the same problem. I made a purchase that didn't seem to work, so I went through the Paypal Pay in 3 checkout process again. Same thing happened. When I checked my account Paypal have listed both transactions as "pending authorisation". I've messaged them but they won't give me a straight answer, just repeating information available on the web. The merchant has no record of my order, and now I'm skint as a result of the duplicate transaction. Here's the message they sent me.
"I reviewed your PayPal account, your transaction of £144.00 is in pending authorisation status. When making a purchase with PayPal Pay in 3, we will place a pre-authorisation hold on your chosen card for an amount equal to the initial payment or one third of your total purchase amount. This will show as a pending authorisation in your PayPal account activity and also in the bank account of the card linked to your PayPal account. Once you complete your purchase with PayPal Pay in 3 and the merchant ships your goods, the pending authorisation will be removed and the initial payment will be withdrawn from your card. If you do not complete your PayPal Pay in 3 transaction, the pending authorisation will be automatically voided by PayPal within 72 hours of the pre-authorisation hold."
But I don't know what is required to "complete" my Pay in 3 transaction, and they won't tell me. I only want one of the orders to be refunded. I'd still like the first transactiont to go through without being "voided".