I was just setting up a store with GST tax on Magento 126.96.36.199 and got caught up on a bug where the tax on a product would be calculated correctly, but the total on the cart page would show it 100x (yes 100 times!) lower than it actually was, leading to an incorrect total being calculated for when tax is included.
With a bit of Google’ing and I found this forum post which had the answer. A clean way of making this little patch while we await a core fix is:
mkdir -p app/code/local/Mage/Tax/Model/Sales/Total/Quote/ cp app/code/core/Mage/Tax/Model/Sales/Total/Quote/Tax.php app/code/local/Mage/Tax/Model/Sales/Total/Quote/ vi app/code/local/Mage/Tax/Model/Sales/Total/Quote/Tax.php
and make the change on line 314:
$rate = $rate/100;
// Removed bug with tax calculation //$rate = $rate/100;
That should fix it, let me know how you get on.