I think that when you start the engine the steps should follow the door regardless of the step override switch (if equipped). So my first thought is your step comes out when you start the engine because the door is open.....or because the magnet sensing switch on the door is not aligned correctly (thinks the door is open)? When the engine is off but the chassis (engine)battery is enabled....does the step come out when you open the door and go back in when you close the door?
Glad your step is working for you now. Perhaps there was a bad connection in the 4 pin connector that you cycled (assume you have the controller model)? The Kwikee Step (Lippert) PDF troubleshooting info can be found on hyperlink (or search via Google for it if the link wont work):