I am assuming output mode should be set to pulldown for external recording on Ninja2 (not fixed) though I'm not sure why. Is this correct?

Thanks. I'm really enjoying using the c100 and have learned a great deal from this forum.

I mean if I am shooting 24P should I set output to pulldown in the camera menu?

I have my camera set to 24P and my Atomos Samurai set to 23.97 FPS. The C100 will always output a 60i stream, regardless of the internal record settings. So the 24P is embedded in the 60i stream. The Samurai analyzes the stream and removes the 3:2 puldown on the fly. Otherwise, you would probably need to set the samurai/ninja2 to 60i and deal with pulldown removal in post.

Does this help at all?