I have now had this problem with two orders. The first one I had to e-mail Customer Support to get it cleared. The second order is still shown as Unpaid after almost an hour after PayPal issued the payment confirmation e-mail. Something is definitely broken here and it's broken badly. Whether it's the new site or PayPal is open to debate but, given that the problems appeared within seconds of the new site layout following a period of intermittent Site Maintenance Outages, I know what seems the most likely.

[EDIT: Just e-mailed Customer Support on this latest order]