First issue was that the Samurai would not receive timecode out of the C300 Mark II. Also, it would not record trigger through the camera. This was solved by using the HDMI to SDI Atomos adapter... pulling timecode out of the HDMI signal from the camera. It worked, but was a frustrating workaround that Atomos should remedy...

Second issue is that the footage off of the Samurai seems to have a black border around it after ingesting the footage into Premiere. I am not editing or ingesting, this is from the client:
"I have a question about the b-roll prores files we recorded on your C300 Mk II (cam 660C).
When I ingested the 660 footage into Premiere, the files all had a black border around them. The resolution and pixel aspect ratio are correct (1920x1080, 1.0). All the image settings look the same as the A + B cam footage. But for some reason there's this weird black border around everything shot on Cam C."

All other cameras were C300 Mark I, and they all worked out fine. Here is a screengrab:
https://drive.google.com/open?id=0B4nVcH2rJCxWalZlUGxZVHBRTzEySWJkUnNKWUdaZE9XcFdJ

Anyone have any thoughts? We backup recorded to cards, they should all be fine without any unwanted borders. Will double check them asap. Editor can always go off of the cards to edit with, but that is a minor pain since the rest of the footage is all in prores.

Camera settings:
1080/23.98
59.94 system frequency
50Mbs file

Only the Rec Out SDI port is for recording from the C300 Mark II. Mon Out and HDMI are for monitoring. What this means is that you had the LCD on the C300 Mark II set to display the HUD around the video (when you press the Display button it goes from Full, to Bordered, to No HUD) and this was sent out to the HDMI port. So if you had to use the HDMI port to record, you cannot use any of the Display options other than Full or no HUD.

What firmware version is the Samurai unit you have?

Ah, that makes sense. Unfortunately, I was not operating the camera and so, when it was recording the display probably was changed. Is there not a clean feed out of the HDMI port though?

We thought we solved our timecode issue by using the HDMI port now only to have this gotcha happen.

The HDMI port is meant for monitoring only or non-critical recording. The SDI Rec Out is what is intended for recording out of.