This issue you are seeing is due to how Linnworks has to handle an unpaid order downloaded from eBay. When Linnworks downloads an order, it downloads the information into xml format. You can see this raw data yourself by right clicking the order and going View > view xml.
Because the order is unpaid, the 'Amount Paid' in the xml is 0. This Amount Paid value is the value that Linnworks uses to represent the total for the order. If the order is unpaid, then Linnworks can't show how much the order has been bought for.
Until the customer has paid for the order, and an 'Amount Paid' value has been added, the order in Linnworks will show the true total of the order, which at the moment is 0.