I use Adobe Media Encoder CS4. One of the most important things with Flash videos is the keyframes. If you don't set your keyframes, then viewers can't fast forward through the videos. The player needs to know what the closest keyframe is to the point in the video you are fast forwarding to. So make sure whatever program you use has the ability to properly set these keyframes. I tried several programs before using Adobe Media Encoder CS4, and the Flash video player couldn't fast forward through the videos because these programs didn't set the keyframes properly.
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