Hi,
Part way through creating the 2.5.x beta series I decided that I should bite the bullet and release an entirely new plugin. I’ll be continuing to update the stable version of the Multi-level Navigation plugin but that beta is unfortunately dead in the water and I won’t be updating it. Sorry about that, I shouldn’t have released it. I’ll eventually be releasing a version of the PixoPoint Menu plugin which updates itself automatically from the Multi-level navigation plugin but at the moment only most of the settings are transferred. The only major thing which doesn’t transfer over if you switch plugins is the menu contents. Your CSS will automatically be transferred over.
The PHP code in the custom code boxes requires the advanced addon which is not yet available for the PixoPoint Menu plugin so you are probably best off sticking with your current beta. There aren’t any major bugs in it so as long as you aren’t experiencing problems with it you may as well stick with it until I release version 2.6 of the Multi-level Navigation plugin which will include a recommendation to upgrade to the PixoPoint Menu plugin for those using the 2.5.x branch (at that point the transition will be seamless).
Hopefully that explains the situation.
I hadn’t originally intended for things to get this messy. Apologies for that.