Just spoke to Customer Service Paypal after discovering no record of a recent sale in my account, despite receiving an official Paypal confirmation email (though with invalid transaction ID) and despite eBay marking the item as paid.

They told me to send the email to phishing, but then called me back 5 mins later to say they are aware of a bug that started around midnight AEST ago (it was infact several hours earlier than this as my problem payment happened almost 24 hours ago). Not only are some transactions not appearing in accounts, but there's an issue with incorrect fees being deducted. If you're a seller you'll want to check your recent transactions.

I was told the issue would be fixed in 24-48 hours and that something would appear on the Paypal website soon, although I'm not seeing anything yet.