Look at the Micro-Manager logs (in the Corelogs folder). It will list the plugins it finds when it starts. There are various reasons why a plugin is not listed, for instance, it could be that you compiled your plugin for Java 8, whereas you are using Java 6 at runtime (JVMs are backwards compatible, but not forwards compatible). Or the jar that Netbeans/Eclipse produced is incorrect. In fact, your observation that no plugins at all are shown in the menu demonstrates that your jar crashes the thread that is loading plugins. There most likely is a stack trace in the Corelog that will give a clue about the underlying problem.