I have a rather large folder of 1921 songs. When I input the folder name as the FLAC directory and output a folder on the same drive called Music Copy, FLAC squisher reports 1921 out of 1921 files completed but the output folder actually only contains an artist's (incomplete) folder and a loose song directly in the folder. I have set it to copy MP3's as well, as not all of my music is in FLAC, but it didn't manage much. Any help?
There was a bug that sometimes caused an error when encoding a FLAC file that contains embedded art. I've fixed this in FlacSquisher 1.1.0; can you try it and see if that fixes your issue?