I am agreeing with Dan's Post #13. Somehow FLAC and Apple Lossless seem to impart a sound on the data. I am not sure if it is in the compression/uncompress action, most experts say no, or is it in the conversion process of getting the laser to read the pits and bump off a CD, then converting that to the digital data that the compression algorithms will be used on.
I do know that my Yamaha HD-CDR1500 which saves CD's uncompressed (bit for bit) sounds better than the MS-300 via either units analog outputs or when the data is sent via both units digital outs to the MCD-500 DAC's. It is not a big difference but it seems to be there.
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