It might be as simple as the primary method you have set in your PayPal account.
You can have PayPal draft your checking account or to use a credit / debit / check card. You can pick the order in which you'd like PayPal to use in order to pay. They will first use any money you have in your PayPal account, then you can decide if you want the charges to go to your card first or you bank account first. PayPal might not show the payment as complete until it gets verification that the transaction was completed from your bank or your card.
I've had my PayPal set up to be Instant Payments drafted from a bank account. It always showed immediately that the funds were sent immediately (PBS was one of the things I'd paid for with PayPal). Then for some reason, unknown to me, PayPal started to call my transactions eChecks (on my bank statement). Maybe they changed whatever they were doing at the beginning of February? Anyway, I had to wait a few days for the "eCheck" to clear and show as posted to an eBay seller.
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