It's doing to same thing with my store; the coupon is discounting the coupon % from the shipping amount even though it is set to the following in the order total module:

Discount Coupon (Sort Order 280) (Settings are:false, false, standard)
Shipping (Sort Order 290)
Sub-Total (100)
Tax (300)
Total(999)

Display prices with tax: false

This is a sample of how it is currently calculating:

Subtotal: $42.00 (correct)
Coupon (20% off): $-8.40 (correct 42.00 * 20%)
Shipping: $8.95 (correct 20% is not being removed)
8% PST: $3.26 (incorrect should be $3.40 see below)
5% GST: $2.04 (incorrect should be $2.13 see below)
Total: $47.85 (incorrect should be $48.08)


The taxes are being calculated as if there is 20% off shipping:
42.00 - 20% = 33.60 (correct)
8.95 - 20% = $7.16 (incorrect, should not discount shipping)
33.60 + 7.16 = 40.76 (incorrect)
40.76 * 8% = 3.26 (incorrect)
40.76 * 5% = 2.04 (incorrect)

I would really appreciate any assistance you may be able to offer me as I am really struggling on this one.