My first and probably totally ignorant thought is that you may have created a ground loop. between the two assemblies.
ground loops (twin ground connections make fine 60 hz hum pickups .Our surroundings are saturated with 60 HZ sine waves.
going back to audio days .... such problems were eliminated by connecting all device grounds to one common point.(ground) or earth
I once made the mistake of looping a ground from one device to another (in a string of devices)
Believe it or not it happened to be an old IBM Selectric printer (flying ball) to which I affixed a printed circuit board of my own making.
Nothing worked , as stray pulses, as detected with a hand held pulse detecting tool, abounded at all points on my ground wires
A quick look at an Arduino controller + 3 phase servo /motor ... shows that the common point of the 3 coils ,
is completely isolated from the controller's ground..(external earth connection)
Am not a software guy but I date back to machine language routines,
but I would guess that if your software routines worked OK before, they should be working OK now
Hope this is not totally off the wall