Use the link in the Namespace Manager to Rebuild All Namespaces, or if that fails, try saving one of the namespaces that isn't showing. It's also possible, but unlikely, that vBulletin "forgot" that you have permission to view some namespaces. This sometimes happened for vB 4.1 when the datastore was saved in Xcache. You can fix this by saving some permissions again, or using Maintenance Tools and rebuilding Forum Information.