Ran across this with Sun Valley Garden Center. When using tax method Sales Tax – Multi (available in 8.4 and up apparently) please remember to add the Tax Area 2 field to the receipt form, customer form, and appropriate doc designs. In the case of tax exempt customers, the Tax Area 2 field on the Customer Form must be set to Exempt, or they will be charged the 2nd tax on receipts.
Note: This new Tax Area 2 field is not yet in DVS Find/Replace. It is, however, in the latest bridge (in case of emergency break glass).