When a Sales order is entered, a transaction number is not allocated to it until you click the Save Action Button.
Once the Transaction is saved, only then will Auto Warehousing commence and start generating Shipments for the Saved Orders based upon the Rules on the Site Table and the Auto Warehousing Task.
If the sales order has been saved, and then modified auto warehousing will kick in again and create another shipment for the modified/additional lines.