Kijanki - I assume bit perfect software/hardware delivery is a given. I am talking about different sound from bit identical files. There is no timing information in a digital file so the jitter comes on playback. There are lots of sources of it, as you say. But, how do you get different jitter from 2 identical files played back on the same system? It is theoretically possible, for example, if one file is contiguous and the other is badly fragmented and you computer and disk drive are really noisy. But if two bit identical files are contiguous and on the same platter on the same drive, some people will still say they sound different. That is the part I just cannot hear. Can you?Are you talking about identical same format files (flac vs flac) or different format (flac vs wav)?
If same format, they should sound the same. Different format, then probably sound different since they are encoded differently even though both are lossless and uncompressed ... different file layout.