Just had the same problem….really annoying.
Jerry Hofmann is right – the problem is probably caused by Final Cuts hostility towards mpeg/mp4 files.
Even when you transcode them to Apple proress they still do not function properly (!!)
I shared the smooth-cam clips to my desktop, then imported them, and put them into the timeline, instead of the clips with the filter on them.
After exporting the whole timeline, it finally worked. The clips were just as smooth, as on the time lime of final cut 7.0.3
Can’t believe final cut fails to export the smooth cam filter on it’s own..