but I don't recall the color flashes issue
Don't know what you mean by this ^. But all the same. My problem has been figured out. And I now know what to do. Strange the things that Adobe get's short sighted about... like BD slide shows, or audio in After Effects that actually works, allowing you to export/encode video clips according to your chapter markers in Premiere Pro (rather than having to create a whole new sequence for each encoded video clip). Anyway. Thank you.