I am having a similar issue with Paypal Website Payments Pro. All seemed to be working fine until the install of the Discount Coupon codes add-in. In my case, when the transaction is passed to Paypal, the Taxes on Shipping is not being added, just item subtotal, shipping, and any discounts / coupons. This seems to be a common issue. The most common recommended solution involves configuring Paypan IPN. However, I'm not certain whether this is something that is compatible with Paypal Pro ot not. I think I may be contacting Paypal directly, as any advice that is being offered is often too vague and doesn't match my setup.