The quick, simple answer is to not use (or ever open) the 2D cockpit view. Try this experiment, load any plane in free flight mode.
You should start off in the Virtual Cockpit (3D) view. If you scroll through the different cockpit views ("A" key on the keyboard), you should notice the mouse pointer start going crazy once you get to the 2D view.
This is the view where the control panel disappears and turns into a blank, black box with only the top 1/3 screen showing the out of the window view.
Is this what you are talking about?  If so, there is a fix that requires some adjustments to the Panel Configure Files of the plane you are flying.