When creating the overlay video in Adobe After Effects use Shift Channels (under Effects menu) and change the "Take Alpha From" to Red,Green,Blue or Alpha. Go to Effects -> Channel-> Remove Color Matting. Then Render your image( you can use H.264 as the output format but make sure to change the Channels to Alpha in the "Video Ouput" section. NOTE: When using the video as overlay, change it's "compositing mode" to Screen and more importantly add Chroma Keyer to the video through the Video Event FX and adjust the colors and contrast to match the color set by you in AE(Shift Channels).