Weblogic Console Problem with pending folder xml's

As u know, weblogic server collects the changes which we did by the consele screen under "pending" folder. But my wl server is not creating that files correctly. For example, each line has an end with the characters 
 (which means\r), it adds xmlns to each element and finally it started to give the error "Caused By: com.rsa.jsafe.JSAFE_PaddingException: Could not perform unpadding: invalid pad byte" when I was trying to create a new datasource.

A simple example for the file structure is below:

    <domain xmlns="http://xmlns.oracle.com/weblogic/domain" xmlns:sec="http://xmlns.oracle.com/weblogic/security" 
xmlns:wls="http://xmlns.oracle.com/weblogic/security/wls" 
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://xmlns.oracle.com/weblogic/security/xacml http://xmlns.oracle.com/weblogic/security/xacml/1.0/xacml.xsd http://xmlns.oracle.com/weblogic/security/providers/passwordvalidator http://xmlns.oracle.com/weblogic/security/providers/passwordvalidator/1.0/passwordvalidator.xsd http://xmlns.oracle.com/weblogic/domain http://xmlns.oracle.com/weblogic/1.0/domain.xsd http://xmlns.oracle.com/weblogic/security http://xmlns.oracle.com/weblogic/1.0/security.xsd http://www.bea.com/ns/90/weblogic/security/samples http://xmlns.oracle.com/weblogic/1.0/security.xsd http://xmlns.oracle.com/weblogic/security/wls http://xmlns.oracle.com/weblogic/security/wls/1.0/wls.xsd" 
xmlns:dom="http://xmlns.oracle.com/weblogic/domain"> &#xd;

as u can see there are 2 xsi attributes in it.

And also, whan I try to add a new datasource, it gives the exception "Console encountered the following error com.rsa.jsafe.JSAFE_PaddingException: Could not perform unpadding: invalid pad byte.". But the xml file is correct(and it is not related with the password encryption)

What could be the problem? Any ideas?