Creation of New Shipments on Inbound

When we create an inbound order, initially, it creates a shipment in return.  This part of the process is okay for us.  But the way our business operates DAILY we will make adjustments to that inbound order after it is keyed in initially.  The problem is that a new shipment is created and put at a status 10, after the original shipment was already put at a status 25 with shipment charges applied in the transportation module.  Is there a processing option or something we are missing to prevent this?