the material cost comes from the sales order invoice file, specifically the BKARHINVL for the line items on the invoice. what happens, is that AT the Time of Posting the invoice, the data is copied from the Sales order files and records created to the Invoice files during which time, the AVG cost from the Item master is taken to update the cost of the Item just shipped.
 
so, if your Work orders are finished after the sales order is invoiced and your items on hand are zero, and or avg cost for that item is zero, then your material cost at invoicing is also going to be zero.
 
thing to do, is make sure the work orders production is finished and posting with a cost, prior to (at least...) Posting the Invoice. ( but don't forget to post the invoice before you try to re release the same sales order if processing multiple shipments)
 
hth