On the fs100, the camera outputs a 60i signal which the ninja2 recognizes and converts back to clean 24p. However, there are a bunch of ways this can be screwed up, for example if you go into the menus with the ninja on, the signal loses sync and you end up recording Maggie's and interlacing.
Anyway my first instinct would be to see If something similar to that is going on. Is the c100 outputting a true 24p signal or 24p wrapped in 60i? If you look closely do you see any interlacing in the footage when something moves quickly?