As a customer, if I placed an order and some items were in stock and some were pre-orders or back-orders, I would not expect the company to ship me everything for free or for only one shipping charge. If I had placed an order only for back-ordered or pre-ordered items, I would still pay shipping. Some sites give you the option to hold everything until all items are in and can be shipped together or pay for each shipment as it is ready. There is nothing wrong with that.
The way you do it is very nice, but I would never expect it. Whatever you decide, just make sure you clearly state this policy on the website.