What is the detected path Minion has for your addon folder (look under options)? Sounds like its being set to your game folder and not the addon folder. If you set the path to the game folder this would happen. If you set the path to the <documents>/Elder Scrolls Online/Live/AddOns folder it will work just fine.
If you manually entered where the game is it wants to know where the addon folder is not the game.
Can you attach your minion.xml located in your windows home/user folder under the .Minion folder?