The nme thing is something that shouldn't be happening, and I can't quite figure out why it does. When stencyl builds a project, it's supposed to remap any "nme" reference to "openfl".
designpeg, did did you overwrite Stencyl in your Applications folder? If you did, could you try installing Stencyl again, but deleting the old copy first? I don't know if that will help, just a wild guess.