I would expect a gStreamer Java API to be using a JNI to connect to gStreamer's native libraries. Running outside of Ignition allows the JVM to use the platform library paths to find and load everything necessary. Within Ignition, you must manage all dependencies yourself. Note that much of gStreamer is GPL code and cannot be distributed in an Ignition module.
Fortunately, once you manage to get a JNI .dll or .so file loaded in Ignition, they will generally follow the platform's defaults to load other native dependencies. You might find this thread helpful:
In my module, I included a config page to allow the user to specify exactly where the necessary external jar and JNI files are located, if not found in the default location.