What is the difference between duplicating and instancing an object, in regards to the materials they point to? As a follow up of my question What does the &#39;F&#39; button and &#39;2&#39; button do (materials tab)?, I have another question:

When I added an object mesh and applied a material, and I added another mesh, not duplicate but with ShiftA, and choose this same material than it is added as a new user (checked by press the 'F'-button and look at the number next to it).

When I duplicate linked an object by AltD their material data are linked, but this duplicated linked object mesh is not added as a new user (checked by press the 'F'-button and look at the number next to it)

But when I change the viewport color of the material then the added objects meshes (with ShiftA) and the duplicate linked object meshes (AltD) do change their viewport color. So are material from added objects linked different then the material from duplicate linked objects?
By default materials are linked to the object data. Hence when you instance the object data you are not duplicating the material, or the users of the material. 

When you AltD an object, you are keeping the same object data.
If you look at the Data tab of the properties window for any linked duplicate object, you will see that the Mesh Data has the number of users.

The material still only has one user because part of the object data is the materials.




However if the material link is set to "Object" then AltD duplicating an object will increase the user count for the material.