How do I avoid a/v sync problems in output files?

Hi.
I wanted to process a video and iMovie 09 doesn't support deinterlacing, so I deinterlaced the video in another program and generated an mjpeg avi (1920x1080), then a wav for the audio. When I import these two into iMovie 09 and paste the audio, everything works and previewing the video doesn't show any problems.
However, when I try to export this through quicktime, the audio gets a half second lag from the beginning which is never recovered through the video. This makes the video useless, as from the first 10 seconds you notice the performers' movements don't match the song (it's a live performance from a music group).
In the quicktime export options I select an MP4 container (no ISMA), H.264 codec, resolution 1920x1080HD, 29.97 fps (just as the source was), and automatic reference frame. The audio options are set to AAC-LC (music), because I can't select anything else.
Is there anything I can do to make this work? Why is it working correctly inside iMovie 09 only?

What kind of video is your source?
Probably the answer is to use a better deinterlacing tool. There are two great tools that are free. (MPEG Streamclip and JES Deinterlacer). THere is no need to create a separate video file and audio file. Use one of these tools and convert to Apple Intermediate Codec.

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