Well, Chrono is five years older than the three girls. It's not that hard to find fourteen year olds who are mostly adults. Especially when they find themselves in situations where they're not coddled.
It was mentioned that the Wraith apparently only shows up towards the end of a cycle; that would seem to point towards the master program and/or the defense program since (in canon) they can't do much until the Book is mostly filled. On the other hand, that doesn't explain why nobody has seen the Wraith in the more recent cycles.
My guess is that there were originally five Wolkenritter and that the Wraith fell victim to the damage that causes the defense program's wackiness. Perhaps the Wraith was able to remember what happens to the Book's master when the Tome is filled and began to act against the rest of the book, or mayhap the corruption simply made the Wraith non-functional. Of course, there's the meta-reason that with the Wraith the Wolkenritter now have a counterpart for Vesta as well as Nanoha, Fate, Arf, and Yuuno Linith.
But if Alicia is capable of repairing it... of course, that implies that the Book has a hardware failure of some sort, rather than a software failure (or that Alicia's new talent goes further than has yet been demonstrated.)