This is a funny problem. You can automate a normal Access session, and you can open an application in runtime mode... Why not automate the runtime application once it's open?
You can start by opening, in runtime mode, a dummy empty database. Then grab the automation handle to that application, and change the current database to your protected application. The code below was tested in Access 2003, so it might not work in your version. It's the entire module of the single startup form of a (third) database; you can do something better in a compiled language (to protect the password).
(°v°)