The invoice created from the sales order does not have the same shipping cost with the sales order

Check the shipping cost in the Item Fulfillment. The shipping cost transferred to the invoice is coming from the item fulfillment not from the Sales Order.

- The shipping cost on the Item Fulfillment is the actual cost. The Sales Order is only an estimate and the actual shipping cost can vary depending on the actual weight of an item or the packages used to ship the item as shown on the Item Fulfillment. This is the amount forwarded to the billing transaction (Invoice/Cash Sale).