I'm not sure what the BD-RE is, but I started a new project, set the problem video timeline as first play, and it started 0:18 seconds in! It is so nice to know what the problem is.
Now I just don't understand why it is happening. We are taking h.264 footage (.mov, 1920x1080 23.976) into Adobe Media Encoder CS6. From there we select the "H.264 Blu-Ray" preset from the drop down menu, then "HD 1080p 23.976" from the next drop down. Then we simple encode. From there it kicks out an .m4v file and a .wav file.
Any ideas?