"Based on AI research, here's what's likely causing your issue:
Likely Causes
1. Known FLAC Encoder Bug in Switch
There is a documented issue where Switch's FLAC encoder introduces loud intermittent crackling and artifacts when converting high-quality WAV files, particularly at 24-bit depth. This matches your symptoms exactly (artifacts + cutting in/out). The problem appears specific to the FLAC encoder implementation NCH uses, not the FLAC format itself.
2. 32-bit Float WAV Source Issue
If your source WAV is actually 32-bit float (common with DAW exports) rather than true 24-bit PCM, Switch's FLAC encoder may mishandle the conversion. FLAC only supports up to 24-bit integer, and some converters bug out when downsampling 32-bit float → 24-bit integer FLAC but handle 32-bit float → 16-bit or 32-bit float → ALAC correctly.
3. Compression Level Conflict
Switch's FLAC encoder may have issues at higher compression levels (6-8) with 24-bit files. The command-line docs show compression levels 0-8 are supported, but bugs often appear at extreme settings.
Workarounds
Since ALAC 24-bit works fine for you:
Convert WAV → ALAC (.m4a) 24-bit instead (you've confirmed this works)
Try FLAC compression level 5 or lower in Switch's encoder options
Use an alternative converter for this specific task:
fre:ac (free, open-source)
dBpoweramp (paid, highly reliable)
Foobar2000 with official FLAC encoder
XLD (Mac)
Verification Step
Check your source WAV's actual bit depth using a tool like MediaInfo or Audacity. If it shows "32-bit float" rather than "24-bit PCM," that confirms the root cause.
This is almost certainly a bug in NCH's FLAC encoder implementation rather than user error, given that 16-bit FLAC and 24-bit ALAC both work correctly with the same source file."
If appropriate, file a bug with NCH.