I found a way to fix this problem (I’m using 4.9.2). After reading this thread, I checked the rotation of the root bone while playing the prototype I’m building, and there is an rotation offset in the root bone with the stock animations for the Third Person example.
What I did was reimport the original animations into the Mannequin in Maya and re-exported them. No need to change anything, just a simple import/export operation. This seems to fix the rotation problem in the root (See the images below).
I hope this helps.