Did you import a video and then put subtitle text over it, to then export? If you did, you don't get the video in the export, only the subtitles. In the export options you want to check the box that says to ignore the stage color and to make an alpha channel. Also uncheck the option to go to Adobe Media Encoder. Then you would take the MOV you get and use another program to superimpose the subtitles over the original video. Premiere or After Affects should be able to do that.
If you run into trouble you could post the FLA somewhere, and I can export it for you.