It seems that the UV Flatten nodes likes edge loop winding in the same direction.
Counter clockwise is Houdini’s winding direction that has normals facing the positive Y direction. This also applies to creating curves as well, if you want the curve’s closed geometry facing up, create the curve counter clockwise.
This problem came up trying to UV a simple rectangle that has bevel applied. By specifying the correct edges but wrong directions, we end up with one of the most stupid UV time toilets imaginable.