I've been playing with both FlAC and WAV this afternoon on my Bryston BDP-1 and I agree there is definately a difference between the two. After lots of back and forth listening, I'm almost certain it is only a slight volume increase on the Wav files and nothing more.
Quality wise, everything appears to be the same and the dynamic range is identical, but the FLAC file plays a little quieter, which gives me more granularity on my volume control, which I like.
Wayne.