I've tried with version 3.06.1, and just downloaded the latest version of the plugin today (3.07.0). When I create an invoice for partial payment using PayPal (yes the IPN is setup correctly), the first payment goes through fine and the invoice properly updates the payment made by the customer. The issue is when the customer goes to process a subsequent payment through the existing invoice. PayPal gives a very basic and unhelpful message stating: "This invoice has already been paid. For more information, please contact the merchant."