Can you provide more details, Which the GateIn version you are using ? Which navigation.xml you are talking about ? you have modifed the navigation.xml of portal.war or in your extension project ?, can you attach your sample ?
In GateIn 3.2, I've just made a simple test: modify the file GATEIN/webportal/src/main/webapp/WEB-INF/conf/portal/group/organization/management/executive-board/navigation.xml
--> Change the node order and it works as expected (Ofcourse it's needed to clean the data to make GateIn rebuild its database from configuration files)