What funds your paypal, Ponyfan? A card or a bank account? I'm not asking for detailed specifics but it might be worth checking with them (unless you use paypal balance only) to see if the balance there has been deducted (ie that it might be in progress) or if something has flagged up and blocked it.
My bank are very safety conscious and if they don't recognise a transaction they are block crazy and I have to contact them and say yes, it's me, and yes, I do mean to pay my rent/for x thing, and please could they let me do it.
So I would check that to see if that's a reason for the delay.
If the website is in the US it shouldn't be an issue but there are some countries which still have to manually accept payments because of currency or other restrictions...that may also be an issue.
If it's your funding source then it might affect your payments but if not it's probably the site and not going to affect those. But you might want to contact paypal and check with them as well if you don't get an answer from your funding source (or if your funding source is paypal credit).
I personally would contact both
But its up to you. It being a major website doesn't mean that it couldn't be flagged as an unusual purchase by someone in the process, so its worth checking out.