Sorry if I misunderstand, but this sounds to me like you don't have Mental Ray activated, because of what you said about the hypershade. (Even if you have had it activated in the past, sometimes it just goes away for fun.)
To activate it though, go to "Window" > "Settings/Preferences" > "Plug-in Manager"
Now, in the new window it's kind of halfway down the list, but make sure you have a check mark beside loaded and autoload under the name "Mayatomr.mll" (autoload makes sure it will load whenever you open Maya again, but it doesn't always stay loaded, especially if you refresh your preferences)
Now, when you have it activated, you can go to the hypershade, and where it says "Create Maya Nodes", click on that and go to "Create Mental Ray Nodes". All of the MIA materials are scattered in different places under the Mental Ray Nodes, so you'll have to look for the ones that you're using.
This should work, because if you saw them available to load in the plugin manager, then I would think that meant they downloaded properly.
However, if when you do use them in the hypershade, and they have a little red line where the name is, that means that it will not work, simply because your renderer isn't set to Mental Ray. If you don't have it then don't worry.
But if you have to set it to Mental Ray, here's how:
Open up "Render Settings". It's the button with the little clapper board and two dots one above the other. It's near the top left of the page. Then under "Render Using" Switch from Maya Software to mental ray.
I really hope that helps. Because as far as I know it sounds like everything is in the right folder.