In the settings menu for shipping, I have the enable shipping checked, shipping rate look-up set at none, the per item shipping and additional charge =0
In the additional settings on each product, I have entered an amount for each product based on the product being packaged taken to FedX and given a cost for the actual freight plus what the client wants to add for packaging and handling. In most cases 13.95 total which is the amount put in for the product which the customer purchased. It doubled this amount.
I am going to make a purchase myself and see what happens and will report back.
I have not made any changes the the php file which is attached per your request.