Unfortunately the detail in those images are too small to see (at least for me) so I am still not clear what is going on. Can you post each of the four shots separately so that they are full size? Or post the one shot full size even if that means scrolling around to view it?
My only thought for now is, if you ignore the select material and do the steps - apply material 1 to the object, render, apply material 2 to the object, render, are the two renders different? Can you share those two renders? I am wondering if it so happens that both materials are rendering the same so no matter which you select the results are the same :) This is mostly because I can't see what the node is that is combining the two materials in the second case before it goes into the select material. Thanks!