How do I get rid of this transform node ?, it was created when I parented my root controller
group to the root joint, see pic. Either one of those nodes have a negative scale.
Transform|228x500
These transform nodes get created when you change parent of a joint and parents have different scale or shear transform values.
In this particular case you can try freezing tranfsorms of Root_CNTRL_GrP
before parenting Root_JNT
to it.