The index tree doesn't show some existing namespaces neither the content inside each of them, althoug you are logged in with permissions. The only way to see all the namespaces is just to do any change using the configuration manager, and then once the changes are saved, the nodes will be shown correctly. The problem persists next time you access the wiki, you must perform again a change in the configuration manager, and save changes in order to see all the index nodes. On the other hand, I have noticed that these hiden namespaces have no other namespaces inside, and the ones that are correctly shown in the indexmenu are those with subnamespaces inside. I'm not sure if the problem is related to indexmenu plugin or Roundbox template, but this problem is not reproduced using other templates.