I have a video iPod 30gt, and I can't play .FLAC -files on it. Apple doesn't support .FLAC, and neither does iTunes. I don't know if there's a plugin for the Windows version, but I'm using Mac Os X, so I have to decode .FLAC -files into .AIFF to listen them on my iPod or iTunes
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I don't know if there's any loss of quality, but the file sizes are fucking too big.