Perhaps this one is already fixed. It seems related to several other bugs reported here.
I was integrating my Grails code into a larger project. I copied the project directory somewhere else, and added the copy as a Content Root, and removed the original. I carefully went through all my project settings and switched everything to the new location.
However, JetGroovy was now confused. Even though IntelliJ was now using the new files, Grails was still using the old ones. I think somewhere the JetGroovy plugin was still using the directory that it created, even though that directory was no longer a Content Root.
Another way state this bug is-- if JetGoovy didn't create the Grails project, it doesn't like it. If you add an externally created Grails projects (even one created by JetGroovy elsewhere) JetGroovy doesn't figure out which files are Domain objects, Controllers, Views etc.