I believe it's because Poser never used to be able to dynamically load morphs into a .cr2, it needed a channel to inject them into. V4 and M4 used the .bat files to insert these channels, but they only inserted the channels for the morph sets you had, which is why you have to reinitialise them every time you added a new morph set. Example, you owned Morphs++ and initialised them. Later you got, say, the creature creator morphs, those channels needed to be added, so you had to reinitialise. A pain, but there you have it, that's why.

As for the disappearing backslashes, you\ can\ insert\ them\ by doing a double backslash where you want a backslash to be.