I'm going to consolidate the list of fixes to a single post to make it easier on people:

a) Edit includes/classes/order.php

circa line 347 - you should see

PHP Code:
'subtotal' => 0,
'tax' => 0,
'total' => 0
which should be changed to

PHP Code:
'subtotal' => 0,
'shipping_tax'=>0,
'tax' => 0,
'total' => 0
b) edit includes/modules.order_total/ot_shipping.php

circa line 67 change

PHP Code:
$order->info['tax'] += $shipping_tax_amount;
$order->info['tax_groups']["$shipping_tax_description"] += zen_calculate_tax($order->info['shipping_cost'], $shipping_tax); 
to

PHP Code:
$order->info['tax'] += $shipping_tax_amount;
$order->info['shipping_tax'] += $shipping_tax_amount;
$order->info['tax_groups']["$shipping_tax_description"] += zen_calculate_tax($order->info['shipping_cost'], $shipping_tax); 
c) For the original group pricing fix, edit includes/modules/order_total/ot_group_pricing.php

circa line 60
change

PHP Code:
if ($this->include_shipping != 'true'$order_total -= $order->info['shipping_cost']; 
to

PHP Code:
if ($this->include_shipping != 'true'$order_total -= $order->info['shipping_cost'];
if (
$this->include_shipping != 'true'$order_total_tax -= $order->info['shipping_tax'];  
if (
$this->include_tax != "true" && $this->include_shipping != 'true'$order_total += $order->info['shipping_tax']; 
d) For the coupon fix, edit includes/modules/order_total/ot_coupon.php

circa line 396
change

PHP Code:
if ($this->include_shipping != 'true'$order_total -= $order->info['shipping_cost']; 
to

PHP Code:
if ($this->include_shipping != 'true'$order_total -= $order->info['shipping_cost'];
if (
$this->include_shipping != 'true'$order_total_tax -= $order->info['shipping_tax'];  
if (
$this->include_tax != "true" && $this->include_shipping != 'true'$order_total += $order->info['shipping_tax'];