The product that we’re working on uses two monitors, Unity is using one and a command and control application is using the other. The Monitor that is displaying the command and control application is a touch screen. When you touch the screen, it is the same as a mouse click allowing the user to manipulate virtual controls. The problem that we are having is that if Unity is running fullscreen (which it needs to be) and you touch the touch screen, Unity will automatically minimize.
My question is, can this behavior be changed? What I’m after is a way to keep Unity maximized even though it has lost focus. I’ve looked through the forums and through the Unity settings and can’t find anything obvious.
Thanks in advance.
I recommend you send an e-mail to Unity support (support@unity3d.com) about this - they can consult the development team to see if anything can be done about this.
any news about this issue? i’m having the same troubles, two monitors. in the first unity in fullscreen, in the second a motion tracker selfwritten that track people in realtime and sends via osc the people position in realtime. but sometimes, unity loose focus and it turns to minimized, no way to mantain the fullscreen, until i restart the app or manually click on the unity app icon in the taskbar 
Still an issue with Unity 3.x unfortunately. Until Unity supports multiple monitors, it’s unlikely to be fixed ( http://answers.unity3d.com/questions/10129/how-to-prevent-a-fullscreen-application-from-minimizing ).