System Information
Linux bubastis 3.18.12-gentoo #1 SMP Tue Jun 16 16:26:19 EDT 2015 x86_64 Intel(R) Core(TM) i7-4800MQ CPU @ 2.70GHz GenuineIntel GNU/Linux
01:00.0 VGA compatible controller: NVIDIA Corporation GK107GLM [Quadro K1100M] (rev a1)

Blender Version
Broken: 2.74

If I attempt to use python to set a per-object material with code like this:

obj.material_slots[1].link = 'OBJECT'
print(obj.material_slots[1].link)
obj.material_slots[1].material = mat
print("argh "+obj.material_slots[1].link)

somehow the material_slots[1].link reverts to 'DATA'

Here is a quick python script you can run while the cube is the active object:

import bpy

obj = bpy.context.active_object

while len(obj.data.materials)<2:
    obj.data.materials.append(None)

obj.material_slots[1].link = 'OBJECT'
obj.material_slots[1].material = bpy.data.materials[0]

print(obj.material_slots[1].link)

Notice how it prints out 'DATA', despite the fact that we set it to 'OBJECT' .