Jaksta/
Replay Media Catcher has a fix flv utility where you can adjust the timestamp. you usually want to go somewhere in between 24-34 to fix it, and then test in vlc to see if it's correct. only prob with this way is if there is any silence in the flv, that part will be fast forwarded when played back.
I haven't found a perfect way of converting, and I've tried a lot of different ways.