Hi,
I had a similar problem.
The customer successfully paid via PayPal but WPEC was emailing they didn't. I couldn't resolve it as it's very intermittent, maybe once or twice every couple of months.
I mitigated the impact by changing the content of the email that gets sent to them.
eg:
"If you selected the "Paypal and Credit/Debit Cards" option at checkout and PayPal accepted your payment then PayPal will send you a confirmation email. PayPal will then notify us of your payment and we will process your order.
If you selected the "Bank Deposit" option at checkout please make your bank deposit payment to ........."
This way the email caters for both types of payments we offer. Maybe you can do something similar.
Regards,
Mike.