Sorry that I was as clear as mud on this. I will try to do better with some pictures.
This picture shows the way it works when I process payment with paypal through my shipstation.com shipping program. It labels shipping as shipping and not as a product see below. This is the way it is supposed to work
So here is the same shipping program but using hikashop with the paypal pro plugin. This one is an example of my problem.
On this one you can see the "shipping paid" first arrow is 0.00, this should be 12.50 but instead if you see in the details look at second arrow it is labeling shipping as an "order item" rather than in the "shipping paid"
This ends up creating problems for taxes, accounting, and confusion with when the labels are printed how many items are supposed to be in the box. I hope this makes things more clear. Sorry it wasnt before.