New York State tax on shipping

In New York State law, when an item being sold is taxable then the shipping component is also taxable.  But when the item being sold is tax exempt, the the shipping is also tax exempt.  If the order contains multiple mixed line items, only the amount for shipping the taxable items is taxed.

Unfortunately NetSuite is calculating tax for shipping regardless of whether or not the items are taxable.

These orders are from our webstore and being imported by FarApp.  The web store is calculating properly, it is only on the import that this is happening.  I do not want to create a special shipping item because of the multiple mixed line item scenario (and the fact NetSuite should follow appropriate tax laws...)