I too have this problem with QBO with several clients I encouraged to go to QBO.   This is a QuickBooks flaw and apparently the programmers never actually worked with Invoice processing with nontaxable business or multi state taxing.

The auto Sales Tax feature someone thought was a great idea does not work with 3rd party integrations.  It creates a nightmare on the ledgers.  Then the blame game begins.

And who ever posted "go into every customer and/or item" change their settings do not understand the complexities and volume that can take place with sales receipts and/or invoicing and integrations with other programs.  

This feature needs to be scrapped and the old system brought back.

Just my opnion