I feel like I'm a broken record here, but it helps to have more info than that...such as what resolution are you shooting on, crop mode or not, what frame rate, how do you process the shots, etc.
Agree 100% It is very difficult to help if you do not provide more information about the settings that you are using to record the video.
Additionally make sure you do this:
You should check that in Canon Menu:
Image Quality = Raw
Auto Lighting Optimizer = OFF
Long exp. noise reduction = OFF
High ISO spee NR = OFF
Higthlight tone priority = OFF
Multiple Exposure = Disable
HDR Mode = Disagle HDR
Also you are recommended to use FPS override, it use to eliminate some problems with frames:
23. Move to the Movie tab and select FPS override with the scroll wheel. (see note below)
24. Press the Q button
25. Change the Desired FPS to 23.97 using the small (top) scroll wheel.
26. Move to the Optimize for with the large scroll wheel.
27. Change to Exact FPS with the small scroll wheel.
28. Press the Q button and then press the Set button (on the center of the large scroll wheel) to enable FPS override
29. Now FPS should read 23.97
And Finally you should upload the original DNG for a more advanced DEV to look at.