Apple is reporting that this may happen with the built-in iSight, and that optimizing video is the solution.
This issue also affects some other video - in particular, some h.264 video. I have some h.624 that was encoded with Handbrake (from AVCHD source). 9.0.4 causes serious audio drift over the course of the video (about an hour). I downgraded to 9.0.2 to finish the project, and have not yet tried optimizing the video.
I generally use Turbo.264 to go from AVCHD to h.264 in a smaller resolution, and to make it editable in iMovie (smaller resolution is necessary to make editing practical, and it is for ultimate use in iDVD). I have not yet tried Turbo.264 output as source material.
It appears to me that the issue with 9.0.4 is an h.264 issue rather than the result of a particular encoder, though it could be limited to video produced with certain encoder implementations. It is another regrettable regression though. The drift definitely carries through to output.