We have run into this issue also. Not sure why QuickBooks on line has to so difficult to manage.  What we are running into is apparently QuickBooks is looking at the ship to box instead of the Customer info. So even though the customer is in the system as tax exempt it still keeps wanting to charge tax. This happens almost every time we type in a customer.  It is very annoying and hopefully will be fixed soon. The old desktop version was much easier and user friendly for sure.