Not really... I'm just using the presets that came with Flash Video Encoder.
But playing around the other day, I did find out that if I use Quicktime files that have been exported from Final Cut Pro using Quicktime 7.2 that it will encode but not properly. I have to open the Quicktime player set the audio to 44.1k and eliminate all but two channels of audio in the export settings and re-export to a new file. If I do all of this, the encoder works just fine.
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Wayne Carey
Schazam Productions
http://www.schazamproductions.com
http://blogs.creativecow.net/waynecarey