I now have the same issue as well on 2017 with stock ebox. Tested continuity on white and black from switches at ebox and tested positive for continuity when pressing stop or pulling lanyard and negative otherwise. Tried grounding white from CDI and that didn't shut it off either. Also tried running additional ground from battery to ebox.
Gave up and adjusted the idle RPM screw so engine would shut off if no throttle applied so I could keep riding and that is working ok.
Anyone figure their issue out, if not was thinking of:
* buying another CDI, likely OEM
* adding a switch in the ebox that would kill power to something so it would turn off, any suggestions on switch and/or what to control with the new switch?