I am having the same problem.  This is a big issue for anyone that does API integration and needs and autogenerated number. I turned off custom transaction numbers and it works from the API until you go into QB Online and create an invoice from there. It then says auto generated and refreshes the invoice screen. Then if you go look at the settings the customer transaction number setting has been set to on again. I develop software for a living. How can there not be a bug for this issue? Or a workaround. There must be some reason that the system changes a system wide setting without consent or prompting? Can someone at Intuit please take a look. Thanks.