Dan, I don't really understand what you are saying, but if you are referring to a case where when you launch the client you are not getting to the login page directly, but have to either acknowledge another page first, or maybe enter a command or other information that then gets you to the login page, auto-login should still work. The auto-login logic keeps looking for a page/screen that fulfils three requirements:
1) The screen has at least two input fields
2) 1st field is a visible input field (username input field)
3) 2nd field is an invisible input field (password input field)
The first time you get to such a screen, the first field will be populated with the username, and the second with the password of the account configured/selected for auto-login. After that it will no longer be active.
Does that answer your question, or did I misunderstand?