Is the format of your original mp4 video progressive or interlaced? You mention the TV show video. I just wonder it.
I used multiple files in a different editor first, Sony Vegas Pro, then I rendered it and put it in After effects and added transitions. I believe it's progressive
Some screenshots would really help us to see the issue.
Are you still facing this problem? If not, let us know how you solved it. If so, please let us know so we can assist you further.