Subsequent ArcGIS Post Installation for Java platform does not update the Server Directories location set by docBase for context/arcgis/server in the server.xml causing Virtual Directories not to be exposed.
Manually edit this file <a href="file:C:/Program" target="_blank">C:\Program</a> Files\ArcGIS\java\manager\service\tomcat\managerappserver\conf\server.xm and update the docBase pointing to new location instead of <a href="file:c:/arcgisserver" target="_blank">c:\arcgisserver</a> then restat ArcGIS Server Manager Service.