The orientation of the scnece is off,...

The world orientation will always remain the same, but the local orientation can be different for bones.

What control are you having issues with?

Ok so the controls work with local space, so even though the World Z is always up, the local Z might not be aligned.

Are you animating the Body control or the Root control?

Either way, you will often encounter controls that have a different orientation to the world.  So world Z (up) might be local Y, or similar.

It might be a little confusing but give this lesson another watch
https://cgcookie.com/course/fundamentals-of-animation-in-blender-2-8x

I hope it starts to make sense.

Hi Tanaka.  That is the exact file I started with in the video

Make sure you are animating the correct control.

I hope this video makes it clearer.