Unless I am misunderstanding something here, I am seeing the exact same behaviour in 2.79b / 2.78c as well.
Could you show us this is working in 2.7x?

This also seems like expected behaviour: If you set this up like you do, you are effectively selecting twice:

• (1) view3d.select [mapped to Mouse > Selection Mouse]
• (2) view3d.select_or_deselect_all [mapped to Mouse > Left]

select_or_deselect_all is just a python wrapper and will [next to some other stuff] eventually call view3d.select as well...

And if you select twice in the same location [without you setup, just in default blender], blender will first select the closest object, for the second click: select the next-closest object.
So if you have two objects this might look like selection isnt working but if you put 3 or more objects in depth you will see blender is still cycling through the different objects.

That being said (and without knowing what you actually want to achieve here), your setup will work as far as I can see if you disable the 'regular' selection keymap item mentioned in (1)

Marking as incomplete until we know if this is solved (or if there is something else going on...)