If the file's MD5 sums can be compared and match perfectly, then the wavs are identical. There will be no difference in the files because they are identical. One cannot sound better than the other because they are identical. If the MD5 sums don't match, then there could be a difference in sound quality because the files are not identical.
Hence why we use the MD5 system to verify that we have perfect copies of shows. The 2 samples, if the have the same MD5s, are exactly identical PERIOD. If you hear a difference, its because you want to. If everything is done correctly, a perfect digital copy is a perfect digital copy (the MD5 verify as so), so any discrepency is all in your head.
Terry