I am trying to create a plugin that loads different resources taken from the loaded project. I am trying to register to ResourceChangeListener of the workspace in an early stage
You should investigate having a workspace save participant to handle situations before your plug-in is started normally. Few plug-ins are important enough to warrant always starting up that early without any user involvement.
http://help.eclipse.org/indigo/index.jsp?topic=%2Forg.eclipse.platform.doc.isv%2Fguide%2FresAdv_saving.htm