Uploading/Exporting from iMovie 11' makes weird black flashes on my video

I have been working on a project for a very very long time. I finished editing and decided to export the file to my mac (I used regular, Quicktime, and Finalcut Pro), when I play the file it will continuously have black flashes every 2-3 seconds. I tried uploading the file directly to YouTube, but I get the same problem. What am I doing wrong?