There is a bug in the Unix/Linux JEE application server code that for some configuration could prevent deep monitoring. The issue will occur if the Application Server path contains a symbolic link or is network mounted. In these cases, the underlying discover code does not see the path on disk, which results in the discovery 'working', but an inability to get monitoring information.
The Unix/Linux JEE Application Server discovery discovers the instance and the task to run deep monitoring completes successfully, but the deep monitoring never clicks on and there are no JEE Applications discovered.
Use the Universal Discovery as outlined in this posting here and here.