Shoutbox

I'm using a third party encoder for videos for my iPod, and I'm able to watch them perfectly, the problem is:

When I update my videos (add/change/remove) on the iPod the ones that I didn't even touch will disappear and I'm only able to see them on iTunes, the new/edited ones show up correctly.

What am I doing wrong? Or what is the problem?

Thank you very much in advance.