This is a JVM related issue. JVM needs write access to the /etc/.java/.systemPrefs directory, which it cannot access when run as a non-root user, see: http://bugs.java.com/view_bug.do?bug_id=4838770
Try changing ownership of the /etc/.java/.systemPrefs directory to the current user [eg. wso2:wso2] using
sudo chown -R wso2:wso2 /etc/.java/.systemPrefs
The file will still be writable by root (as root can write to any file), but if you need multiple users to be able to write to this file you might set up a file ACL as well using:
sudo setfacl -R -m u:wso2:rw /etc/.java/.systemPrefs
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