Sounds like you have paths for the ESD to get into one or more of your microcontrollers. ESD does a great job of trashing the proper code execution on a microcontroller.

Also it may be that even though you have apparently done a lot to provide isolations, maybe there is still some path that ground noise from the stepper motor operation is getting into one of the microcontrollers and causing a software upset.

It sounds like you have a job here for using a high speed DSO to track down where the noise is getting in so that you can then address adding clamping, filtering, or further isolation as necessary.

Michael Karas