Perfect Source
It is important to have a perfect source before you start compressing.
One thing to keep in mind, sounds obvious, but it stills manages to confuse good number of you according to your letters.
You can't "fix" MP3 by recompressing it to FLAC (or any lossy to lossless). You just cant, audio is wasted and the data is lost. Same goes for recompressing MP3 from lower to higher bitrates (for example 128kbps to 320kbps). Because the original information is already lost, this operation (often termed as transcoding), can't improve quality of your audio file and is more likely to degrade it. All you're doing with such recompression is increasing size of your file, and that is in no way useful.
So, for the perfect FLAC file, you need to have clean perfect source.
If it is some song you just produced it will probably be that way, if you are ripping from audio CD there's work to be done, just be patient and read on.
