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Two things to consider when doing frame captures, the rate of capture and the resolution. Viewing your capture config, it show a limit of 1 capture max. That one capture seems to be at a different time than your video screen capture. (See bee in flower in frame capture not present in the video.) So colors and shading may be different. You may want to set capture to once ever X secs and compare those times with the video. Also, validate that your video encoding profile does not have color parameters set, which may be different than the frame capture.
The resolution of the frame capture is typically lower than the video. This would provide a lower quality and averaging of luma/chroma over a large section. In this case, it seems that no resolution is set, so it would use the source resolution. Is that the same resolution as the video?
Please see the following link for Frame Captures with AWS Elemental MediaConvert. https://docs.aws.amazon.com/mediaconvert/latest/ug/file-group-with-frame-capture-output.html
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I've updated the original post so you can see that it is the very same frame and the colors differ. You mean my encoding profile originally? I mean whatever the original video has set, that's what MediaConvert should generate thumbnails from, no? I'm not sure what color profile it is, I'm just using hevc_videotoolbox to scale down whatever the user supplies, is there anything other I need to do? The resolution exactly matches my input video and that is what I'd like, I'm using this as background while the video buffers intially, so the different colors are very noticable. The video comes out in correct colors, but the thumb does not