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Why are you encoding through Video Charge then re-encoding on your server with FFmpeg. FFmpeg is total crap for FLVs; H.264 is okay because they use the x264 library.
Why not encode your videos to FLV VP6 using On2 Flix or Sorenson or Adobe Media Encoder, and then put them directly into your server without additional re-encoding. The videos will look much better, at a lower bit rate.
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