at the time the EndLabelProcessor is executed there shouldn't be any layerless nodes.
Could you do me a favour and export the layout graphs? Our website has some information on how to enable debug files and where they will end up. Could you activate those, execute layout once, and post the files somewhere?
Oh, that's interesting. I only looked at the current master and couldn't see anything wrong with it, but had forgotten all about the pull request. That will be fixed in 0.2.1 once that is released (we haven't decided on a release date yet).