Sorry. Having two plugins is utterly stupid.
If the PixoPoint Menu plugin works fine for you, then use that. The Multi-level Navigation plugin will eventually be replaced entirely.
There was only supposed to be a short transition period when there would be two plugins, but I’ve had quite a lot of troubles getting the PixoPoint Menu plugin to work consistently across various setups, and I haven’t gotten the time to write a flawless Multi-level navigation to PixoPoint Menu plugin converter.