We are using the prism and WPF to build application. Recently we started using UI Automation (UIA) to test our app. But some strange behavior occurred when we run UIA test. Here
stukselbax, try to find a sequence of keystrokes (TABs, and an ENTER most likely) to click the button that enables you to see the items. it is pretty easy to send keystrokes and i can add more in here about that if that works for you. you can always establish a tab order in your application that makes the most sense for users.
------ Update on 6/20/12 --------
Have you tried double clicking a shortcut to your app on the desktop using PInvoke to see if you can see the controls when it is opened that way? Here is a link to an example here on stackoverflow:
Directing mouse events [DllImport("user32.dll")] click, double click
Another idea: some of the controls on the app I am currently automating don't show up in the tree until a mouse click occurs on them. To accomplish this without using any hardcoded coordinates, I find something in the tree which is just (above/below/etc) the place where I need to click to get the control to appear. I then get the mouse coordinates for that item and put the mouse at a small offset from there and click. Then I can find my controls in the tree. If the app is resized, moved around, etc. this will still work since the small offset is still valid.