Hello, I'll take any theories on this.
Basically when the FLVs are opened in a player, the playhead doesn't go back to the start of the clip. It always begins a few frames in. I've re-encoded a thousand times (from movs). Any ideas why this would happen?
As you may know, Flash video can only play from, pause on, and navigate to full frames in the video stream. Depending on the encoding this can be from every 3d frame to every 15th frame. The other frames are 'made up' and can't be viewed individually. This is how temporal compression works, in any format. It's a tradeoff - you gain a lot in general quality. Now, I'd certainly expect that the first frame in a video is a full or 'real' frame; it's logical. It doesn't seem to have happened here though. I assume you are using the built in player, and not one you've constructed yourself in ActionScript? My advice then would be to add little bit at the start of the video in your editing app. Copy the very first frame there (your intended start frame) and stretch it out (you may need to use a bitmap) a few frames; I'd suggest 5-10. When you export this, the encoder may still - for some strange reason - put the first full frame not as the very beginning of the stream, but at least it will be inside the chunk of similar frames you've made. Somewhere. Hopefully this will be good enough.
Not everything that can be counted counts, and not everything that counts can be counted.