Board Thread:Theories and Speculation/@comment-3568954-20150523051244/@comment-4912646-20150526063530

Elveonora wrote: No. More correctly, chakra is blue anime because Pierrot decided so. But in recent images, Kishimoto also colours it blue sometimes, as if he can't decide whether to use his original colouring or the anime's. The most obvious example is of course volume 67, but I think the previous artbook also included separate images where Naruto's Rasengan was coloured yellow and blue.

As for why their chakra modes differ from other jinchūriki, I am now convinced it is a result of the unique mechanics of the Four Symbols Seal and/or the Eight Trigrams Sealing Style. Retsu no Sho's bit on "Kurama Chakra Mode" specifically notes that the markings of the Four Symbols Seals become visible when Naruto enters that mode, finally confirming that the black markings are in fact the seals spreading over their bodies, so without those there wouldn't be a Nine-Tails Chakra Mode, or at least it would look radically different. The chapter where the mode debuted was called "A New Seal", after all.