Hi,
garylucas is right, can we see inside the controller.
The layout of the wiring is important. If you have separated the 230V inlet supplies you have gone a ways to prevent conducted interference.
If you have a cable carrying significant current like a spindle motor lying next to a signal cable carrying a few mA or less then the more powerful
cable will induce noise into its neighbour. Ideally you would separate the VFD/spindle and stepper wires from the signal wires. The stepper motor
currents don't seem to be giving you any grief so don't sweat them too much but you will need to separate both the 230V input cable to the VFD and
the cable to the spindle from the VFD from all the little signal wires and by several inches if you can.
The signal wires include the multicore parallel cable from the PC to the BoB, the Step and Dir plus Enables to the stepper drives and all the home
and limit switch wires. If you choose to use shielded cables earth only one end of the shield to one common earth usually at the BoB end.
For electrical safety you should earth the spindle motor back to the same common earth point along with the power earth. It is very important to
NOT accidentally earth the frame or other components of the machine with either shields or ground referenced signal wires, you will create a
ground loop which will induce noise into all the signals and drive you absolutely stark raving mad....I know...that's how I got to be like I am!
Craig