Apologies for not getting back sooner.
I may have fixed this problem by setting up PayPal Instant Payment Notifications. I went to PayPal/MyAccount/Profile/SellingPreferences/InstantPaymentNotificationPreferences and followed the instructions from Woo at http://docs.woothemes.com/document/paypal-standard/#section-3.
I'll write back if I experience the problem again, but maybe this will fix Scruffy1's problem.
Susan