FLAC is a lossless compression format. It is possible to hear differences between FLAC and WAV files when played because your computer is decompressing on the fly. But if you take a WAV file and make an SFV of it. Then convert the WAV to FLAC and back, the SFV will match. The file will sound the same when played. It is the exact same file. Different programs can also sound different while playing the exact same file.
Now two WAV files may sound different depending on the way they were created. Just because the file is a WAV or FLAC does not mean that it is lossless. It is the same thing on an Apple. It all depends on the way the file was created in the first place as to whether it is truly lossless or not.