I'm assuming when you say' the amplified files' you are referring to files that you have amplified in WavePad?
Could you give us just a bit more info - when you look at the original files' waveform, does it have any spots where it comes close to peaking?
If you amplify a file to any degree that sends parts of it past 0 dB (peak) then you will get distortion.
Converting it to flac is secondary; you'll need to get it mastered properly first (do whatever necessary to trim peaks so you can amplify it enough), and if the original file is in good shape,
it is likely that you can do that with WavePad.