A core Magento fix for if you have negative subtotals on invoices after applying at least a 100% discount to the order (but the customer has to pay shipping).

negative_subtotal_on_invoice.diff

diff --git a/app/code/core/Mage/Sales/Model/Order/Invoice/Total/Tax.php b/app/code/core/Mage/Sales/Model/Order/Invoice/Total/Tax.php
index 25bbcc7..38587f4 100644
--- a/app/code/core/Mage/Sales/Model/Order/Invoice/Total/Tax.php
+++ b/app/code/core/Mage/Sales/Model/Order/Invoice/Total/Tax.php
@@ -47,7 +47,8 @@ class Mage_Sales_Model_Order_Invoice_Total_Tax extends Mage_Sales_Model_Order_In
             $orderItem = $item->getOrderItem();
             $orderItemQty = $orderItem->getQtyOrdered();
 
-            if ($orderItem->getTaxAmount() && $orderItemQty) {
+            // Need to check if we've got tax or hidden_tax applied to the item so that we calculate the row subtotal correctly
+            if (($orderItem->getTaxAmount() || $orderItem->getHiddenTaxAmount()) && $orderItemQty) {
                 if ($item->getOrderItem()->isDummy()) {
                     continue;
                 }

Thanks for the fix; I've entered it an prioritized in our backlog.