While this may be an old question, the problem is still occurring these days, and the exact question is still not answered properly.
It is important to note that some projects have multiple classes with a main method.
In my case, I could run the project via the main class, but I could not run a particular other class that had a main method. The only thing that helped me was refactoring the class and renaming it. I've tried:
The only thing that let me run this class is renaming it permanently. I think this must be some kind of a NetBeans bug.
Edit: Another thing that did help was completely uninstall Netbeans, wipe cache and any configuration files. It so happened that a newer Netbeans version was available so I installed it. But the old one would have probably worked too.