I am still encountering this issue. The animation played by a Humanoid set to R6 is the same as the AnimationController, but a Humanoid with a RigType of R15 fixes this. The mesh is a skinned custom character created with the Setup button in the Avatar tab of Next Gen Studio.
AnimationController:
Humanoid R6:
Humanoid R15 (Correct):
The arms don’t seem to animate properly at all. The animation is the standard R15 idle animation.