Imported FLAC audio has stutter in beginning

I noticed when you are working with imported FLAC audio tracks in shotcut, the audio kind of chops for a split second. Only happens with FLAC, WAV and other formats had no issues at all. Any way to fix that?

I do not think I am hearing that. You can Use Properties > menu > Convert to Edit-friendly. Alternatively, I suggest to remux that to a mkv file using ffmpeg ffmpeg -i your.flac -c copy your.mkv and try that as the raw flac file format is sometimes problematic.