I made a scene with two renderlayers. One with 3 planes with a movie on it and the second one with glowing streaks.
When rendering the scene with RGBA, because I need to overlay it on a movie in FCP, only the first layer shows up in the rendered file. But they both show up in the renderwindow of Blender. As when using only RGB I get to see both layers rendered well in the rendered file. I tried Animation, H264 and TIFF they all gave the same result.