Magento's current behavior when creating partial invoices, is to bill the entire shipping amount of the order on the first invoice, regardless of how many items have been invoiced.
This is problematic when products ship at different times, which can happen frequently if a store drop ships often. Here is an egregious example:
A customer purchases two products, a Widget that has Free Shipping, and a Gadget that costs $100 to ship.
2. The Widget ships first, so we must invoice the Widget.
3. When we go to invoice the Widget, we do not want to invoice any shipping, because it was eligible for Free Shipping. However, Magento does not allow us to specify how much of the shipping should be included on the invoice, so the invoice includes the shipping amount for the entire order.
4. When the Gadget ships, we go to invoice it. There is no shipping charged on that invoice, because it was all charged on the first invoice for the Widget.
5. Customer and Accounting frustration ensues.
The ability to specify a partial shipping amount on an invoice, up to the total amount charged at the time of order, would solve this issue.