Hi,
Maybe the problem is the Qty Structure Date defined during the costing run.
When you run product costing, you have to indicate what is the validity date to read the structure of your product.
Could happen that you have modified your BOM starting from 31.03.2016. In this case, if when you run product costing, the date entered to read the structure is 30.03.2016, you will not consider the modification done on 31.03.2016.
Kind Regards,
Mariano