Thread is getting old but finally figured out another not so obvious (at least not so obvious to me) issue I kept running into.
Material Slots can only be deleted from the ‘bottom up’
For example, let us say that my character has 5 materials, and I decide to get rid of material 3, I can empty the slot BUT i need to move materials 4 and 5 up one so that the empty material slot is at the bottom,
What I do most often is move the bottom most material (material 5 in this example) to material 3, and reassign the textures to the material slot as well as to my LOD slots. THEN I am able to click the white X’s to remove the material slot I no longer need!