Well the problem is that the layer break isn't actually a layer break.
Let me explain this a bit, the so called layer break is actually a bit stating there's a discontinuety on the disc (meaning that the next stream is alligned properly with the current).
Unfortunally this same bit is also used to handle multiangle stuff (take a look at the original starwars vobs for example).
On the movie only copy we could safely remove that bit, because all we where keeping was one angle and no layer break. In the 1:1 copy this is a bit tricky'er because there's no real 100% safe way of predicting that a layer break is actually the layer break or just a merge point of two angles.
Therefore the only way to remove this, is doing it by hand with ifo edit. Ofcourse we are trying to find a way to work around this, but for now there's not a real solution.