Reproduction steps:
1. Open the attached project "RootMotion Bug.zip";
2. Open the Test.unity scene
3. Observe that there are 3 cubes:
Cube 1 has the Root motion option turned on the animator UI
Cube 2 has the Root motion option turned on and the script to control the Root motion is applied
Cube 3 has the Root motion option turned off (which is not visible) the script to control the Root motion is applied
4. Play the scene
5. Observe that the Cube 3 is stuck in a loop.

Expected results: if the Root motion is disabled, it will be handled by a script.
Actual results: If the Root motion is disabled and the script is applied, the animation is handled completely differently.

Reproduced on: 5.5.3p3, 5.6.3f1, 2017.1.0p3. 2017.2.0b5, 2017.3.0a2.