Change order status alters Order Total

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We have a strange behavior and can't track down the reason/culprit when changing the status of an order.

We get orders with the status as confirmed with the completion of the payment gateway.

When we ship the order, we normally just list the orders on the screen via the Orders listing and using the Dropdown status box, change it to Shipped. This seemed to work fine.

One of the users changed the method because she wanted to look at the whole order and used the Edit Order to change the status to Shipped. When we do this, the Order Total is now just the amount of the Freight/Shipping amount.

So say an order total was $105.00 with $100 being merchandise and $5.00 being shipping. When you edit the order, the total of the order is now just $5.00. This new total of course is throwing off the reporting as well.

Any ideas? Also, how can we get back the original order and paid amounts?

All of our orders have a subtotal of zero, why would that be? We have an order, for example, with 6 line items. These are product variations and individually their price is 0.00 but their parent item price dictates the total. So the order total is $100.00 plus 6.00 shipping, but the Order shows 0.00 subtotal, Freight 6.00, and total Order $106.00.

I think this is why changing the order status from Edit Order alters the entire order total incorrectly. I've attached an Invoice (which incorrectly shows VAT which may be a subtotal? but we don't use VAT) and the Order details screen from the admin. back end.