Magento – Magento saves a wrong order total amount and put the order in Subspected Fraud

PayPal doing the following math: Subtotal + Tax - Discount and receive a Total based on this calculation. While all the figures in Magento sales order are correct there is no way to properly send this amount combinations since PayPal expect calculations made based on prices excluding tax, not including (in your example discount is applied on amount including tax, this is where the difference goes from!). The only way to receive a proper amounts in this case is to pass only subtotal field with Grand Total value, otherwise we will need to change discount to excluding tax which will confuse the customer.

So, to summarize this part:

   protected function _getOrderData(Mage_Sales_Model_Order $order)
        {
            $request = array(
                'subtotal'      => $this->_formatPrice($order->getBaseSubtotal()),
                'tax'           => $this->_formatPrice($order->getBaseTaxAmount()),
                'shipping'      => $this->_formatPrice($order->getBaseShippingAmount()),
                'invoice'       => $order->getIncrementId(),
                'address_override' => 'true',
                'currency_code'    => $order->getBaseCurrencyCode(),
                'buyer_email'      => $order->getCustomerEmail(),
                'discount'         => $this->_formatPrice(
                    $order->getBaseGiftCardsAmount()
                    + abs($order->getBaseDiscountAmount())
                    + $order->getBaseCustomerBalanceAmount()
                ),
            );

Needs to be replaced with (Haven't tested it):

protected function _getOrderData(Mage_Sales_Model_Order $order)
    {
        $request = array(
            'subtotal'      => $this->_formatPrice($order->getBaseGrandTotal()),
            'invoice'       => $order->getIncrementId(),
            'address_override' => 'true',
            'currency_code'    => $order->getBaseCurrencyCode(),
            'buyer_email'      => $order->getCustomerEmail(),
            ),
        );

This is really a bug and should be fixed (we get this occasionally). But the workaround we use, which does not appear to break anything, at least in our case, is:

• Look at each of the orders, especially the invoices tab
• Accept the order with the correct invoice amount (in our case it has always been the one with higher increment_id)
• Delete the incorrectly sized invoice directly from database (tables sales_flat_invoice and sales_flat_invoice_grid)
• Delete the order directly from database (tables sales_flat_order and sales_flat_order_grid)
• Manually verify the stock status of the products included in the order