The problem with Mulder's definition of "ghost" (which of itself is entirely reasonable) is that it isn't shared by the general population. Therein lies the danger of misunderstanding. Suppose I decided to group together all of the processes in the natural world for which we do not yet have an explanation, and label them "miracles" so that I could discuss them without offending the religious. Would that be helpful, do you think?
Terms do tend to shift in meaning, becoming appropriated by those with a particular agenda. For instance, "UFO" is entirely inoffensive, simply meaning that something has been observed in the sky which the observer was unable to identify. There are zillions of UFOs around, quite literally (mainly because most people have not been trained in observation). But if you say that you believe that UFOs exist, it is often assumed that you believe in alien spaceships piloted by little green (or grey) men, on the hunt for loose humans to abduct and do unspeakable things to.