I recently had an issue where a customer was importing sales orders into Dynamics NAV 2015 from their website using a third-party interface module. Shipping charges were being created as G/L Account sales order lines. The orders were being processed using the Lanham WMS and E-Ship modules.
The problem was that when the Lanham Pack Line Scanning close order command was given, the packed item lines were being shipped and invoiced correctly, but the the shipping charges were being ignored stopping the sales order from being completely shipped and invoiced.
What I found was that Lanham have modified Codeunit 7324 Whse. Activity Post (function; InitSourceDocument) to set the Quantity To Ship to zero if the function AllowInWarehousePosting() of the Sales Line table returns false.
The fix was to set the Shipping Charge field (field number 14000701) to true on Sales Line records for the shipping charge lines. Note; the Shipping Charge field is not available on the Sales Order Card so will require a customisation if the shipping charge lines are to be added manually.