We need workflow, design, and render details? What is not working? If you are using a mask to create transparency then you can't use an MP4 file because MP4's only have RGB channels and 8-bit color. You would have to render an alpha only copy of the MP4 and the color copy and let the client use the black and white alpha only copy as a matte for the color version.
If the mask just doesn't show up then the easiest and fastest fix is to load the MOV file into the Media Encoder and render an H.264 MP4 using a preset that matches your video's frame size and distribution platform. The MOV to H.264 conversion will render at the rate of several frames a second.