Anyone seen this before? When payments are passed to Paypal via the Paypal Express module it seems they aren't passing the flag to capture automatically sometimes (it's an intermittent problem, but Paypal have confirmed the data they get doesn't have the flag). This then means the client has to capture it manually on Paypal, which in turn means that Magento doesn't get a call back to generate an invoice for the order, and because the order on paypal is marked as paid any attempts to generate a paypal invoice respond with an error that there's already an invoice tied to the order.
If anyone has any advice on this it'd be appreciated. Paypal have said they aren't going to support it because the error seems to be in the module rather than their service
I suggest you check the IPN URL in PayPal settings - this is the URL PayPal uses to send information about captures to Magento. Maybe if you configure it it will help at least generate invoices on manual captures (usually it's something like domain.com/paypal/ipn/).
I'm having the same issue and my provider magestore.com tells me the issue is with PayPal and PayPal tells me its an issue with the store. Totally irritating, wish someone could get this resolved.