Never used a CNC4PC BOB, the one I use is a PMDX122, I first got one for the Bridgeport I converted and it worked very well so I got one for the next Bridgeport, one for the Lathe, one for the coilwinder and one for the mill I am now doing and all have worked flawlessly for me.
It definitely seems noise from the VFD is an issue but as it has also given problems without the VFD running your issues go deeper. Your 5v signal wires really need to be shielded and the shielding grounded at only one end and all grounded to the same point.
As a test however is it possible for you to disconnect the limits from the BOB and change the active state in Ports and Pins and see what happens there.
Hood