I think you're mistaken about what it's doing. It always calculates tax on the subtotal first. And then separately also calculates tax on shipping if you've turned that on. And then it combines the two numbers, which is probably why you're interpreting it as "adding in shipping".
So, I suspect it's probably calculating tax on shipping because you've told your shipping module to calculate tax on shipping.
Go into your shipping modules and change the tax class to --none-- if you don't want tax on shipping.
.
Zen Cart - putting the dream of business ownership within reach of anyone!
Donate to: DrByte directly or to the Zen Cart team as a whole
Remember: Any code suggestions you see here are merely suggestions. You assume full responsibility for your use of any such suggestions, including any impact ANY alterations you make to your site may have on your PCI compliance.
Furthermore, any advice you see here about PCI matters is merely an opinion, and should not be relied upon as "official". Official PCI information should be obtained from the PCI Security Council directly or from one of their authorized Assessors.