[DEL]IIRC, FFmpeg currently doesn't support RGB H.264 output with libx264 yet (correct me if I'm wrong). It'll convert RGB24/BGR24 to YUV444P before feed to libx264, maybe that's why there's a difference.[/DEL]
EDIT: I'm wrong. You can output RGB H.264 with this command line:
Code:
ffmpeg.exe -i %RGB_Source% -c:v libx264rgb -qp 0 -pix_fmt rgb24 %Output%