If you are using multiple forms of input, you really owe it to yourself to update your version of NGUI. NGUI 3.9 completely revamped the way multiple forms of control get mixed together, simplifying everything greatly. It will also automatically hide the mouse when you start using touch or controller-based input. It shouldn't be too difficult to adapt the current version of NGUI to Unity 4.3.
It didn't use to do this and is extremely annoying.