Hm, if it’s working, it’s working.
It could be, that you have double Vertices, or so, but that’s hard to tell from just your description that Clamp Overlap messes up the inner Bevel (usually it would be the other way around and enabling Clamp Overlap ‘stops’ the Bevel Modifier from working after a certain (sometimes very small) Amount, while disabling it can cause “a mess”).