Handbrake help

[dread]

I'm trying to recode a blue Ray rip that is in h.264 format. I have got this to work on a bunch of DVD rips but for some reason with the blue Ray I'm getting video that does not have sound then another 4 hours of sound without video. In other words the sound and video are there but they are not overlapping. The video plays fine in iTunes before trying to convert it to iPad format. Even happens when i try to encode it to apple tv. Any ideas?

 

[dread]

any ideas on this.