The problem could be with the .FLV file, sometimes there could be problems while encoding any video file(AVI,MOV,MP4,3GP,WMV) in to .FLV format that results in skipped frames. Try your code with some other .FLV file if that works good then you need to re-encode your FLV file.
You can also try capturing the video Complete Event by tracking the Video Playback Progress.
import fl.video.*;
var player:FLVPlayback = new FLVPlayback();
addChild(player);
player.skin = "someSkin.swf";
player.source = "http://someDomian/some.flv";
addEventListener(Event.ENTER_FRAME, enterFrameHandler);
function enterFrameHandler(event:Event):void {
if(player.playheadPercentage>=99)
{
//On Video Playback Complete Actions here
}
}