I’m confused by your description. By “set-up levels” do you mean the NTSC pedestal? What do your chapter marks have to do with transitions or titles?
I speculate that you have clips in different codecs, and/or your render codec is different from your clips’ codec(s), and that you are seeing different color and luminance levels when you export your program by reference or self-contained to some other application. If that is the case, try re-rendering with the same codec as your clips, or export to QuickTime movie with the Color Range set to whatever your other application is expecting.