How to reproduce:
1. Open the attached "zProject" project and "AnimatorBug" scene
2. Enter playmode, click on Sphere (in Hierarchy) and view its Inspector settings, notice that Animator component is enabled
3. Try to press "red" and "green" UI buttons in game to change Spheres Material, notice that the Sphere doesn't react to it
4. Click on "stop animator" button
5. Click on "red" and "green" UI buttons, notice that Sphere Material now changes accordingly

Expected result: Material should change, even though the Animator component is enabled
Actual result: Material does not change when Animator component is enabled

Note: This issue only happens with an Animation Controller that has a Material animation. Issue appears even if this particular animation is in a null state (is not playing)

Regression introduced in - 5.6.0a1
Reproducible with - 2017.2.0b2, 2017.1.0f3, 5.6.2p2, 5.6.0a1
Not reproducible with - 5.5.4p2

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This bug is by design:
Not a regression. The animation format has changed from 5.5 to 5.6. If the animation is made properly for 5.5, then the behaviour is the same.

The Animator writes every value it's bound to on every frame. This is to avoid values staying in random values when changing states.