Are you doing full disc copy? CloneBD doesn't handle 3D copy yet, only SBS/OU or full disc with 2D output.
i had to check my own post again too. I overlooked the "d1" and read it as "3 D", now since you're using a protected iso, could you try the original disc too and see if that works. That way we can find out of it's the protected iso that's "to blame" or it's actually CloneBD thats "choking" on the disc somehow.