Right now, your level 25 character is wearing a Cloak of Order. Looks like a New Monarchy cloak, so all of your Vanguard and Crucible reputations are going to New Monarchy (vendor in Tower North). That isn't a bad thing if you like their items. Also, each level past level 3 will give you a package, just like Vanguard and Crucible. If you want to start gaining your reputation the default way, wear a class item that doesn't funnel rep to a specific class.