Short answer is that the NetBeans Griffon plugin doesn't work very well with latest versions of NetBeans. This is due to changes made back in Griffon 0.9.5 on how dependencies are resolved.
Griffon doesn't really need an IDE but if you must then allow me to suggest you IntelliJ IDEA; the community edition comes with a Griffon plugin that works much better.
But you still have to resolve dependencies out side of IDEA, that is, calling the griffon --integrate-with --idea
command from the command line, every time you update BuildConfig.groovy
or install/uninstall a griffon plugin on your project.