There is a video showing the problem described below however I don't want to post it publicly. If you need to see it to diagnose our problem let me know how best to get it to you.
1. Adding a reel to my cart and you can see that the Air Freight Surcharge has been automatically added.
2. Highlighting the total, which is $132.29
3. The coupon field reads "Change your coupon code" instead of "Add a coupon Code"
4. I paste in a $50 gift certificate coupon code and click save
5. I highlight the coupon code that the system accepts, but the total is still $132.29
6. I confirm the order and go to paypal. Paypal lists the correct, discounted price of $82.29
7. Confirming the order and going to paypal creates a pending order that I can test with.
8. I open the order in the backend and highlight that the $50 coupon was added and the discounted total is correct.
So everything works fine, it just doesn't display properly in the shopping cart, which I'm thinking is a result of a conflict with the Air Freight Surcharge "coupon" being used.