There are some things, apart from the obvious like a grounded shield on the low voltage wires & keeping them away from the VFD output.
You can add a three phase choke to the output (Hammond sell them) and the three phase conductors from the VFD to the Motor should all be twisted together. Is your DC supplies referenced to the ground plate also? also it pays to ensure the PC DC common is well grounded. especially if you are using a desk-top PC instead of a industrial type. I usually build my PC's into a cabinet and the PC motherboards usually have a couple of the mounting holes that are at DC common and I make sure these have metalic screws through to the metal chassis.
Make sure you have a ground from the VFD as well as the motor that goes to the common ground point.
Good luck, I know from experience these problems can give you a royal head-ache.
Al
CNC, Mechatronics Integration and Custom Machine Design
“Logic will get you from A to B. Imagination will take you everywhere.”
Albert E.