There shouldn't be differences between flac and wav as both are lossless. You might want to check if both sources were played back with the same decibel level. USB is a different source from CD and the dB levels should be exactly the same to compare both. In most head units different sources can have different level settings. I know I can adjust each input on my HU.Thanks. I did exactly what you said. But used Switch Sound file converter to convert the Flac files into 16bit/44.1 wav files.
I still noticed a difference. Not as much as the 320kpbs songs vs CD.
Some people say its a placebo but I definitely heard a difference in CD vs. Wav.
I would say at most a 5% difference but it was still there.
But as a musical source signal it shouldn't differ. As long as both files are in the same format, for example 16 bit 44.1 khz.
Most precieved differences come from playing 2 tracks at a different dB level.
The loudest usually gets the vote.
If you take a 16 bit 44.1 khz flac, convert it to wav 16 bit 44.1 khz and back to flac 16 bit 44.1 khz the file should be exactly the same.