Well... Keynot 6.0 is out. But it has the same problems! When exporting the timings of my trimmed Movies are ignored and the presentation is exported with every movie played back from the beginning, and not as they playback on screen. It is a shame indeed that Apple has not corrected this after more than a year.
Have you forgotten your valuable community?
Should we professional speakers switch to some other solution that just does what we expect it to do?
I think I have found a workaround:
In Keynote 6.0 I have "Reduced file size", which basically reduces images and crops the videos to the size you want to playback as defined in the (difunct) inspector. This allows you to re-export the movie, now without any edits on the videos, which basically exports everything with the right timings.
Still just a workaround, but I hope it helps someone