Timecode for PIP video?

[MrAngles]

I'm working on encoding The Matrix Blu-ray with the In Movie Experience picture in picture video included. The problem is that the pip video doesn't play constantly, it comes on in segments, then disappears between clips. When using avisynth overlay to encode the video files together it leaves a black box on the screen in between clips rather than disappearing like it does when played back from the disc.

What tells the Blu-ray player to stop displaying the pip window when it goes black? Is there some kind of timecode file in the mt2s or playlist file that controls this or something, and how can I access it? I sure don't feel like going through the video frame by frame to determine where to start and stop the pip video.

Let me know if this makes sense and if it's in the right section.