This has been an ongoing issue for me, and I’ve been unable to solve it. Setting the global preferences on the website does nothing. Tell me, are you having the issue when you book direct with Delta, or does it happen when using a corporate travel engine like Amex Travel? For me, it happens only with the corporate travel engine. The fix is to immediately log into your specific trip after booking and manage your upgrade preferences for the individual trips by removing the middle seat option. You must do that on the app, because the website does give you the option to select specific seating preferences. It’s a complete joke, but it’s the only work around I’ve been able to find.