The xml files and the sleeper blocks look ok. So I don't know if that's a problem with the editor (to be honest, I don't think so).
@layarion
I don't have time for an detailed reply atm so this must be enough.
1) That's already planed.
2) Are you talking about a list of hotkeys? (I think I am going to implement configurable hotkeys very soon).
3) Ok, makes sense.
4) see 3)
5) That's a technical limitation atm.
6) Is already implemented (tool -> replace layers from ... to... with layers from ... to.
7) There are plans for this feature.
8) Probably. There are a few problems though, e.g. auto-save would be annoying if you work with very big prefabs.
9) The middle mouse button is hotkey for the block picker (it doesn't change the current tool and works with all tools/modes).