What is happening is that if we use the Nav Pane Transfer button to "transfer" an order to an invoice, it puts Avatax in the tax schedule ID. It does this for EVERY order. We then need to go open the "order" and select default under the tax ID and it sets the tax correctly.
Dynamics GP 2013
A fix is provided in Avalara AvaTax for Dynamics GP 12.00.105.00 or later