This is your problem, at least I highly suspect it is. I have seen way too many crappy 6.4 liter programmers take a shit and cause exactly what your saying, I.e, a key reset will clear it up for a bit.
The best course of action is to have the customer return it to stock (this usually takes care of it on your end because they dont want to do that and they will just go away) so you can eliminate the aftermarket stuff as the problem. Or have them reinstall the programmer if a flash or get a new one all together.