So, I won an auction and proceeded to pay for it. After waiting some hours for the confirmation mail I decided that I should contact the seller + ebay/paypal since the charge just wasn't showing up. I haven't had a single answer from ebay nor paypal. Item still shows up as "paid for " in eBay and everything looks like it's working but when I log into the paypal account there's nothing there.
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Did you manually enter your card information during checkout? If so, it's possible you may have paid via guest checkout instead of logging into your account. If that's the case, then you should have received a payment confirmation email separately and I would consider it paid for.
If you didn't receive a confirmation email, and you didn't enter in your card information during checkout, it sounds as if the eBay checkout didn't make it through all the way. You have two options on how to proceed.
The first would be to mark the item as not having been paid in your My eBay and completing checkout again.
Alternately, you could double check with the seller and ask them if they have received payment. If they haven't, ask them to send you a new invoice so you can make the payment.