Hi Brian,
You didn’t make it clear in your post, but are you using Media 100i or Media 100 HD? If it is the latter then it sounds like a mismatch between media & render codec settings. Check that your render codec is set to the same one that you used to capture/import the media in the timeline.
On the timeline Media 100 smooths out the differences between codecs on the fly, but this doesn’t happen in the Self -Contained export option.
If you can’t get around the mixed codec thing, try rendering a title across the top of the whole timeline and then exporting again, or use the Quicktime export function.
Hope that helps
K