My suspicion is you may need to contact Greg of SS, on this issue.
External motion pluigns have Movement buffers in them, so that they can continue
moving while M3 is looping (this is so motion does not stop, or get jerky).
The shuttle pro, his just an HID device, it just sends commands to mach3 per event and that is it.
Mach3 then handles the info. So if your jogging the shuttle pro is sending jog command to
m3 engine strucs which in turn the external motion plugin picks up what you want to do,
it then sends that motion amount/buffer to the external devices buffer.
In a motion plugin, the device developer will need to handle all motion and I/O
that his device handles, i.e. Jogging, Estop, etc...
I suspect that given your situation, there is some kind of logic in the motion plugin that is not clearing
the "left over" job motion, or not cancelling the jog command or process in the device or device plugin.
NOTE: Greg is VERY, VERY good about looking into stuff like this, also, "Jeff Brit" is the Raining king as far as all things Smooth Stepper, as far as a user and OEM reseller & support. I would go to the Warp9 web site, and post your questions on the forum or email Greg (or Jeff) from here, or that website. Both of those guys are TOP SHELF and will get to your issue, especially a safety issue.
Caviot: Greg uses FTDI chips for his USB, I have done other plugins for other OEMs that also use FTDI chips, and we (Greg and I) had a collision. I spoke to him about it, and he figured out what was the issue and fixed it on his end. It has been a long, long time since I fooled with the SP3.0 plugin, and I would have to dig it out if the issue is NOT on Gregs end.
Scott