Hm, this is an interesting one. When the route was complete, did you go through the credits (or skip them) to return to the main screen, or did you load up a save before that point? That's the only thing off the top of my head that might cause this, but I'm going to send it over to my programmer so he can take a more thorough look. We'll definitely get to the bottom of this!
I'm really sorry you're having this issue, especially when you're right at the finish line -_-