I have the exact same problem. This has broken our integration with Quickbooks online since the new invoice layout was released in December. Custom transaction numbers will not stay off. I have tried contacting support, spent multiple hours on the phone and submitted a feedback request with no progress. Quickbooks should be able to generate an invoice number. This is not a complicated thing. I turn the setting off, but as soon as someone opens an invoice in QB online, the setting is re-enabled.
