Your FLAC library is an investment in sound quality. Don't let inconsistent gain ruin the listening experience. With the tools and techniques above, you can permanently fix FLAC gain issues and enjoy your music the way it was meant to be heard—loud when it should be, soft when it should be, but never jarring.
Solution: These files were likely encoded from different masterings or were "remastered" with dynamic range compression. ReplayGain cannot fix poorly mastered audio. It only adjusts volume, not dynamics. Your fix is to find better source files.
find /path/to/music -name "*.flac" -print0 | xargs -0 metaflac --add-replay-gain (But be careful—this treats your entire library as one giant "album," which is rarely correct. Always scan per album folder.) foobar2000 is the gold standard for audiophiles on Windows. Its ReplayGain scanner is fast, accurate, and offers a preview.