I have a little issue with the tax calculation, too....
The Zencart tax is always lower then the manual calculation, or QB.
On an order with a subtotal of 18.60 a 6% tax should be 1.12 and not 1.10 as it is in Zencart. my settins for calculation are as follows:
COD Fee ot_cod_fee
Discount Coupon ot_coupon 280
Group Discount ot_group_pricing 270
Gift Certificates ot_gv 840
Low Order Fee ot_loworderfee
Shipping ot_shipping 200
Sub-Total ot_subtotal 100
Tax ot_tax 290
Total ot_total 999
And this is about every time... always a penny or two short on taxes.