I think I've found the quickest workaround for this. Have a bunch of programs open and goto Logout. When you logout, make sure you uncheck the "Reopen windows when logging back in" and Logout.
Next time you come back, feel free to open as many windows as you like but this time when you logout choose the Shift + Option + Command + Q key command to logout. You'll notice you won't get a window popping up asking you to uncheck because this Forces a Logout.
Because this Forces a Logout - the System Defaults back to the way you logged out the way before.
So just keep doing this key command option and for now it's a quick fix.
So far it's worked for me. Obviously if you forget to do this and you do a normal logout and forget to uncheck checkmark, you have to do this process all over again. Just remember the Key command option will default back to the previous last Logout.
Hope this helps. Let me know if you get a different result.