2009 VNL647 W/ Cummins, Idle Control Issues

Firstly, thanks for providing a forum to hopefully find help. No, I myself am not a trucker, but a good friend of one and I am riding as a co pilot with him. I don't claim to be a trucker, though after my DWI goes away, I plan on pursuing a career in the industry. I grew up around rigs and am familiar with a lot of the mechanics and parts of them, however we've come across an issue that I've never experienced or heard of before, and I'm hoping I can find advice and answers here so we can get the problem resolved before the rig becomes damaged needlessly.

On to the issue,
When the engine is shut off using the ignition switch, it shuts down normally with no problems, but when using the idle control while sleeping, when it shuts off on its own, it sputters 4 or 5 times in a row before it finally shuts down. I'm not sure exactly how to describe the issue, but it seems like somehow, even though it is supposed to be cutting off, it still gets another shot of fuel, which in turn makes it attempt to keep running for a split second, and it happens several times before it actually shuts off all the way. It is very violent when it does this, it shakes the whole truck pretty intensely, much harder than a regular shut down with the ignition switch. From my prior experience with any internal combustion engine, I know the severe jarring like that cannot be good for seals or bearings, or anything else for that matter. I am assuming that the problem is caused by some form of electrical issue concerning the brains of the beast, but I am not sure and neither is the driver. I don't think it is a mechanical problem, as there are no leaks of any kind, at least not externally. Under the hood is rather immaculate for having over 550K miles on it. Any leaks would be immediately apparent.

As far as the shop history goes, according to the maintenance logs, it has been serviced properly and regularly for its whole life, at least concerning the basics (filters, fluids, etc) but more in depth problems, like the mysterious coolant leak that can't be found and this sputtering issue have somehow always managed to be ignored by the company shop. Driver has reported the sputtering issue repeatedly to the shop guys, and they claim they've never heard of any such problem and don't know anything about it, but they won't bother to hook up a diagnostic machine and run some tests to see what's going on. My goal for this post is to hopefully gain some insight as to what the problem is and where a good place to start is so that maybe the information can be relayed to the shop so they can fix it before anything too terrible happens and leaves us stranded in the boonies or something.

Any information that might be suggested is greatly appreciated!