I dont even know what an ESS is, but your description seems to say you are using the wrong polarity for the vfd on signal; can you REVERSE (invert) the meaning of the bit that turns on the vfd? seems when something in control or wherever reboots or turns off, it leaves this bit in the state you have described to TURN ON the vfd: you want this power off state to default to vfd OFF not on....
so, yes, t iwill be a mach3 setting in pins and things or whatever screen it is where you set the inputs up - there is an invert button you can pick. then change meaning on the other side too (in vfd, set that ON input to INVERT to match).