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.