Orders not marked as complete, misc. charge still open

I was cleaning up old open orders and noticed that many orders had a shipping charge on them still open. Instead of zero, there was the extended cost of the misc. shipping charge and the line item shows and incomplete.  This makes the whole order incomplete.

After researching a bit I see that the shipping charge appears on the invoice correctly.  I believe what is happening is that if a charge was added by accounting while invoicing it will be pushed back to the sales order.  However it never gets marked as complete.  

Looking at the OEORDH table, the complete field =2.  In the order through sage I can see that the last detail line of freight is showing as not complete, and appearing in the order total.  Further it is grayed out so I can not change the status to complete.  I can however zero out the charge to make that part correct.

What can I do for the orders in the system that should be complete but are held open by this charge?  How can we avoid this for future orders?  Sometimes we have to add a charge at the time of invoicing, I don't see why this should create a problem.

Thank you!