I just upgraded to 5.3.1 and downloaded the Unity UI Samples package. I loaded up the 3d Menu scene and alas the menu is not there. I think the menu is there but the visuals are not.
I noticed this disappearance with a VR app I was working on which I had built a 3d menu using the UI samples, which led me to import the UI samples into an empty project for testing
Any ideas?
I can confirm, it’s the same with me.
For me, Menu 3D (UI part) not showing up in Unity 5.3.1f (Windows 8.1)
I’ve tried the suggestion to look at the animator for the main menu, but it seems to be ok. The scene and particles show, but the UI elements seem to be invisible. The canvas/panel are there in the editor but again, the actual UI elements appear to be invisible.
So same situation as you.
This is actually really easy one to fix. the problem here is that the core menu has been hidden under a sub root where it doesnt belong. as such it impossible for it to display the menu as it essentially cant locate it.
To fix try moving the Window section under the canvas section out of the MainMenu. DO NOT move it under anything else or it will break the whole lot and you will have to reset the project back to default as it breaks the linking completely.
see attach image to get clearer idea of what im saying.
See in the Hierarchy the Window item has been relocated out of the MainMenu onto the canvas. all of it should function properly without any other changes 
Hey sanjitmatharu, thanks for helping with the 3D Menu error, but when I followed you steps to fix it, I had the settings menu overlap the window. Please test and let me know if you get the settings window overlapping the main window, and how to resolve this issue. Thank you.
Just encountered this myself and yup, overlapping windows…
