I'm having a similar issue but there's too much GST being calculated. I have "Add tax to item" selected, but as soon as I add an item I set up as untaxable like Shipping, it adds extra GST. Not the % amount it's programmed to add either, just a few cents more than I have calculated by hand.
I think I got around it by editing the amount of the untaxable Shipping item to be a few cents less so the grand total at least matched my written receipt, but that's no long term solution to the problem. Any ideas?