An invoice has a tax code of X with Y levels (agencies), but the Sales Tax with that ID in Sage 50 has Z levels (agencies)

Verify that the "Sales Tax Option" is checked on the Manage Accounting Package Setup Table.

Verify that the number of levels on the Tax Code in Manage match the number of levels in the Tax Code in Sage.

If you made any changes to the Tax Codes, verify that the Invoices have been refreshed (Open/Save/Close/Save)