Looks like the video is not in the same color space as the background you have.
When converting to h264, in your video editor, look for a checkbox to preserve or embed color profile. If there's still a problem, try making the compression quality higher. The colors may be getting changed as a way for the compressor to save space.
When I inspect the videos in Adobe Bridge, the color profile for both the mp4 and webm are "untagged".
Cool motion graphic by the way.