This is because the player(codec) is not able to the same justice to both the filesAnd about wav vs flac, I personally always found wav files are far better in audio quality than FLAC. There is no confusion.
Wouldn't this be the best way to A:B WAV and FLAC through the same chain?
The same chain will always mean, the FLAC to be decompressed (all in real time to what ever - loss-less or with-loss), converted to WAV and use the same codec to play as used for the other original wave file.
If both match up, then the playback processes are different.
This is what I had been trying to Convey since AAaaaaages!!!

Manoj, you are my Savior!
....My turn Over.