I am trying to create a room-scale 1:1 VR experience for HTC Vive using Unity and VRTK.
I have a 3m x 3m tracked space for testing, and in Unity I have created a 3x3 room. However, the walls in my virtual world do not run in parallel with the Play Area chaperone bounds – they are intersecting the chaperone. Have a look at this image:
How do I transform my world space so that it's always in sync with the chaperone bounds?

As far as I know the chaperone bounds should always be centered at world space zero coordinate and aligned with the world axis if the SteamVRController is in the root of the hierarchy. Are you sure that you are not making it as a child of another object?
You can also check that the dimensions of the tracked area are the one you are expecting by doing something: