It's only turned black twice; once at VotE1 when he first unleashed his CS2, and once against Juubidara. And of course, we have Darui's unexplained "Black Lightning," which does not appear to use either Senjutsu or (lol) Hagoromo chakra. So obviously black lightning can come about several ways.I think his chidori only started turning black after he got ms. now im not 100% but maybe its black because he adds ameratsu?
The unfortunate result is that it further supports the common misreading among fans as to when Sasuke is using "Senjutsu" (Chakra mixed with Natural Energy, as with the Curse Mark) and when Sasuke is using "Rikudou Sennin Jutsu" (which translates to "Sage Jutsu" sometimes, hence the confusion). Basically, people assume that Sasuke using Hagoromo's chakra = Sasuke using Senjutsu (Natural Energy). This current thread is dangerously close to revisiting that same issue.
As for Sasuke's Chidori turning black as a result of Amaterasu, that simply isn't the case... adding Amaterasu (or rather, Kagutsuchi) to the Chidori simply adds black flames. He used it against Naruto for their final clash in VotE2, but never used it before then.