Something to think about... I actually read something a while back, written by someone on an admissions commmittee, talking about the reason for their secondary fee. One of the big costs of the app procces for them, if I remember correctly, is simply paying people for their time. If multiple people are really familiarizing themselves with your application (multiple LoRs, all of your activities, all of your essays, and perhaps some extra snooping around your app), and taking the time to really discuss it, this might be where a significant portion of that $100 is going.
That isn't saying anything about the issue of whether they actually review your app after a certain date, though. For me, that's a bit more troubling...