In Mixxx 2.1.0, FLAC files are decoded with a -6dB gain. Tested on Linux and Mac.
The problem is reproducible always. Eg, create a 440Hz full-scale sine in both WAV and FLAC formats with "sox -r 44100 -n a440.wav synth 20 sine 440" and "sox -r 44100 -n a440.flac synth 20 sine 440". The WAV file plays correctly; the FLAC file will play at -6dB.
Looks to me that the problem is in soundsourceflac.cpp, in void SoundSourceFLAC::flacMetadata(const FLAC__StreamMetadata* metadata), in the code:
m_sampleScaleFactor = CSAMPLE_PEAK
/ CSAMPLE(FLAC__int32(1) << bitsPerSample);
Since FLAC samples are signed, a FLAC full-scale sample will only reach bitsPerSample-1, not bitsPerSample (eg, in a 24 bit stream the maximum sample magnitude would be 1<<23). This means that m_sampleScaleFactor is out by a factor of two, hence -6dB.
I think the code should read
m_sampleScaleFactor = CSAMPLE_PEAK
/ CSAMPLE(FLAC__int32(1) << (bitsPerSample - 1));
I /thought/ my FLAC files sounded quieter! Thank you very much for the detailed analysis! (Do you use GitHub and want to make a pull request so you get credit in the commit history?)