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Apart from the latest version (0.0.9y) of ffmpegx, is there any other free flv encoder which is worth a try?

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It looks as though Evom should do what you need. Here's a useful post from thriftmac about Mac video conversion apps:

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Handbrake works well for converting FLV to MP4 or any other format that you would desire. Handbrake is usually used for converting ripped DVDs to other formats, but it can also be used to convert FLVs too.

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There isn't much that's available for the Mac, unfortunately.

Once piece of software that I've seen someone mention was Prism (haven't tried it myself, though)

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