Try grounding the Smooth Stepper GND pin (on the external power supply header) to the PC case.
A sure way to create a ground loop. Never do so unless it is the only thing that seems to work.
The inverter is installed together with gekos, breakout board inside second PC cabinet.
Installing a VFD in close proximity to other controls is just asking for problems. They are VERY, VERY noisy. Many commercial machines will place a VFD in a separate control cabinet to mitigate such problems. Using proper isolation, wiring and grounding techniques will help but sometimes relocating the VFD is the only option.