I think this is a case of the hitachi not unlocking the game partition, if you're trying to rip it directly through your 360 drive. I had to use the hotswap method with an old DVD-ROM computer drive to rip discs since my Hitachi was doing the same thing to me, where it only sees the first couple megs (the video partition).
Correct me if I'm wrong, but as I understand it the Hitachi does not support game partition unlocking.
When the SS merger lines are red that just means the values for your file's SS and the "required SS" don't match up. Supposedly the database for finding out the required SS is down so you won't get that half of it to match up with anyway, so you can probably not worry too much about the red lines if you know the SS is good.