Many people find it difficult to debug gstreamer pipeline written in gstreamer java. Only thing you need to do it to set GST_DEBUG environment variable e.g. on linux boxes it can be set by export GST_DEBUG=3 (r whatever debug level you want).
After this is set the just run the java application pipeline. You will see all debug messages printed. HTH.
After this is set the just run the java application pipeline. You will see all debug messages printed. HTH.