The reality of Ghost Poo is actually very simple and explainable by science. But in order to get to the reality of Ghost Poo, I must first make a brief jaunt into a cutting-edge area of modern physics, String Theory.
String Theory, in essence, is an attempt to explain all of the itsy-bitsy particles known to science. Particles like the electron and the proton are known to most schoolchildren these days, but modern scientists know of an entire alphabet soup of particles like fermions, muons, pions, boobions, honkions, and bajeebions. String Theory explains that all these exotic particles are actually vibrating strings, so small that not even an eagle with a microscope can see them. The tough part about String Theory is that in order to make the heinous theoretical mathematics work out, there have to be at least 10 dimensions in the Universe, and puny humans can only perceive 3 dimensions of space and one of time. So the theory says that the "extra" dimensions are really there, but they're so small that not even the aforementioned eagle can see them.
This theory is exactly correct.
So now you're probably beginning to see how String Theory is inexorably linked to Ghost Poo. When the Ghost Poo disappears, it does not really disappear - what really happens is that, due to a rare anomaly in the space-time continuum, all of the poo particles are spontaneously folded into the "extra" dimensions that are undetectable by humans. The Ghost Poo is still there, you just can't see it! You know it's still there, though, because generally just enough poo particles remain in your detectable dimensions so that you can still smell it, and that smell is definitely poo.
That's one more mystery of the universe down the toilet, courtesy yours truly, Baba Doodlius.