I dont remember but it was once said that the seal by minato on naruto was designed in such a way that a bit of kyubi's chakra to mix with naruto's
http://www.mangahere.com/manga/naruto/v11/c091/12.html
What i am guessing is now he has gotten used to kurama's chakra so much that it strting to mingle with his and hence the strange effect. Unlike them being separate (maybe)