Are you using Receivables 9.0 & OE 8.1C? Does your order have a ship-to address? Is your customer tax status (0) a non-taxable status?
Then consider that a major change that occurred with the data conversion for ship-to addresses in the last updates. Ship-to addresses all have an assigned tax status that overrides the customer tax status in AR to accommodate shipping into different tax areas as the destination usually determines taxes applied. When your ship-to addresses were converted they were all assigned a default tax code and that code is your tax status (0). If this code is non-taxable, the order will not be taxed. There is a brief warning about this when the ship-to address is loaded saying that header info may be changed as a consequence of loading the ship-to address but the tax status change may be missed.
The easiest way to correct the ship-to tax status is to export the list to Excel, sort the list correctly and change the status for each group. Make sure you export all the necessary fields needed for re-import and then import the list back into Receivables.