Ok, I can see what is going on here. In your cart file you have two shipping rules and one tax rule. The problem is that your tax rule is being based on the shipping quote value. You need to base this on a percent of the carts total, not the shipping quote.
You have two fedex shipping rules. They are both set to the shipping quote value, so in effect you are doubling the shipping cost. You should remove one of these shipping rules and update the tax rule, it should then be charging the correct amount for these.
