This always happens to me too, and since i cram in so much Special Functions, it throws me off. For instance, when I just created a new function, I go to save the game, I save it, I return to edit the new function, but it's been shuffled so I have to find it first.
So, yes, I've noticed it too. Any idea on why this happens? I've gotten used to it, so it's not to much of a problem anymore, just wondering.
EDIT: [my one-hundredth post! Not that it means anything, I just happened to notice it.]