A WAV file is created with SoundforgePro 10. Encoded to FLAC. Then the FLAC file is decoded. The resulting WAV file has the same audio samples but the file length and MD5 checksum differ. Note: if the second generation WAV file is reencoded to FLAC and then redecoded, the third generation WAV file will be identical to the second generation WAV file.
I have not investigated why the file lengths differ. While this may or may not affect sound quality it does tend to undermine faith in the FLAC process.