Resolution:
In BWC 5.5.1, customization steps [ Chapter 7 Customizing the Collaborator Desktop Interface : Replacing Layout Images > Customizing Logos ] for changing the logos/ Header image have been changed  from its previous versions.   Instead of modifying the layout templates, engineering has introduced the "<!--  skins templates --> section in tibco_service_config.xml" (located under \tibco\bwc\5.5\bui\archive\WEB-INF folder) to avoid multiple files changes.   This change is not yet documented in BWC 5.5.1.

With BWC 5.5.1, we only need to modify "tibco_service_config.xml" file and not any template files.   For eg: To change the  tibco logo to some other custom image, we have to change the ‘name’ and ‘ContentURI’  attributes in the following XML tag

<!--  skins templates -->
&ltcreateTemplateItemFolder name="skins" templateType="com.tibco.ps.model.template.TemplateType.SKIN_TEMPLATE">
&ltcreateTemplateFileContent  name="images.logo_tibco.gif"     contentURI="/PortalTemplates/bui/img/logo_tibco.gif"/>

After seting the path of the custom image at "contentURI" rebuild the Application/project EAR  and  Deploy the newly created application ear.