Pixelate effect when converting MOV to FLV via FFMPEG
You should explicitly specify a video codec using -vcodec as well as quality settings.

The problem is that ffmpeg's defaults aren't very sensible when you only specify a container format for the output, often choosing a sub-standard video format by default.

If you want H.264 output, try using the presets, e.g. -vcodec libx264 -vpre max. (To see what presets are available, try ls /usr/share/ffmpeg/*.ffpreset.)