Try checking the option below on the basic options tab within Transaction Pro Importer for QuickBooks:
Clear Transaction Bill to/Ship to Address when importing
Selecting this option clears all transaction address information before creating the transaction. By default TPI fills in the customer bill to and ship to information when creating the transaction. While this works well when only specifying the customer on a sales transaction (estimate, invoice, sales order, sales receipt), it can cause duplicate address lines under certain conditions. Selecting this option assures that the address lines on the invoice match those actually being imported.