This might take care of the issue of double paying

app/code/community/Bitpay/Bitcoins/Model/PaymentMethod.php

@@ -175,6 +175,10 @@ class Bitpay_Bitcoins_Model_PaymentMethod extends Mage_Payment_Model_Method_Abst
   }
 
   public function MarkOrderComplete($order) {
+    /**
+     * The order has already been invoiced and has already been paid, this
+     * code leads to having payments applied multiple times.
+     *
     if ($order->getTotalDue() <= 0) {
       if ($order->hasInvoices()) {
         foreach ($order->getInvoiceCollection() as $_eachInvoice) {
@@ -190,6 +194,7 @@ class Bitpay_Bitcoins_Model_PaymentMethod extends Mage_Payment_Model_Method_Abst
     } else {
       Mage::log('MarkOrderComplete called but order '. $order->getId() .' has an outstanding balance that has not been paid.', Zend_Log::WARN, 'bitpay.log');
     }
+     */
 
     // If the $_bpCreateShipment option is set to true above, this code will
     // programmatically create a shipment for you.  By design, this will mark