After making self-contained movie, any strobe or slo-mo effect image
becomes jumpy once self-contained. We are using the standard media 100i codec
set to highest quality. Even when set to lossless, problem still exists. Any ideas???
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.