I believe that this is caused by using riivolution and the phantom wings file patch code. I think if you load the game through Gecko Launcher you should be fine. I was having this same problem yesterday. If you want to fix it, you need to get the codes you had before, or you could edit the code and just take the phantom wings file patch code out.
Hope this helps.
im using a similar method to Gecko for loading the games and the codes, i have it in a USB D: