Problems with transcoding a DVD to APPLE TV format

Hi all,

I'm trying to encode a short film I made to submit to a film festival that prefers to have the films sent digitally. So they want the film in the Apple TV format (Mp4 / H264). They recommended using Handbrake (freeware) for this purpose. My problem is this:

When I encode the DVD with Handbrake I get 01:10 min of colorbars before the film starts playing. Now, this in itself isn't the problem (I could easily trim the color bars away) the problem is that the audio for the film starts playing approx. 00:30 min in (over the color bars) and when the picture finally comes on, we've basically lost the first scene of the film (it starts on scene two where scene one is replaced by the color bars).

I tried playing the DVD in DVD player on my Mac and it works fine (the film plays immediately without the color bars). Then I tried playing the disc on my standalone DVD player and it also works there. I went into the Video_TS folder on the DVD and tried playing the .VOB files using VLC and then the color bars appeared again.

Is this something which is in the architecture of the DVD and if so, how can I get rid of it so that I can get the first scene playing properly?

"Two things are infinite: the universe and human stupidity; and I'm not sure about the universe." - A. Einstein