Ground induced noise between two connected boards
My first knee jerk reaction is that the ground connection between the controller and the motor doesn't belong there.  You have a isolator block, which makes sense, but then you defeat the isolation by tying the grounds together.

What is the nature of the STEP and DIR lines to the motor controller, and what exaclty is the isolator block?  Most likely the isolators are opto-couplers.  In their simplest form, these have floating NPN transistor collector and emitter outputs.  If the motor driver has passively pulled up inputs, then tie the isolator output transistors between the motor driver ground and these lines.  There are other ways they could be hooked up too, but it makes sense to get into that after you explain the electrical interface to the motor driver and what exactly these isolators are.

In no case should there be a connection accross the isolation.