FLAC is not the problem. Period.
Period. Period. Period.
So, I read the article while dousing my head with water to keep from flaming in this post because I really wanted to put some thought behind what I wrote. I performed the following test ...
1) Downloaded a 24/96 WAV file from http://www.2l.no/hires/index.html.
2) The FLAC 1.2.1 release to perform a WAV-FLAC-WAV transormation at both compression levels 0 and 8.
3) Given, orig.wav (the original, downloaded file renamed), orig-flac-wav-0.wav (the transform at compression level 0), and orig-flac-wav-0.wav (same thing at level 8) ...
4) ALL FILES ARE PERFECTLY IDENTICAL. This includes both the WAV header and PCM data. (I used a Linux/UNIX command called "diff" to verify this as well as the command md5sum from GNU coreutils 7.6).
What, if possible, could I conclude from this?
1) If I played back the files and somehow all of the files in step 3 sounded differently I have no way to attribute the differences to the FLAC step. I could have very well copied the files and renamed them without ever using FLAC and it would have turned out the same results.
2) If somehow the files in the article *ARE* different and that's the reason they sound different then it must be the utilities creating the files themselves that are in error, not FLAC. FLAC is a perfectly lossless system given my tests. Perfect.
Maybe I sould author a letter to the editor but I just wanted to get my own test results out there for someone to comment on.