VLC Player: effects and filters not working with mp4 videos
have you tried different version? I have no issue on effects ubuntu 16.04 vlc 2.2.2 Weatherwax I have it running well. SO can you please post details of video and effect you were trying. best will be if you post/ point to exact video or very small part of video so that it can be reproduce.
To get detailed info about video file try this tool called mediainfo with this switch --fullscan so that we can figure out.
mediainfo --fullscan video.mp4
feel free to remove some private info.