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I have a similar issue, but only when headphones are on (does not happen on the speaker). I get a very loud CRACK! in between of each two songs (mp3 in Walkman only. FLACS in TC seem to work fine).
It seems that turning on/off ClearAudio+ does not help in this case. I have tried 3 diffrent headphone sets (stock ear-plugs, closed on-head headphones and Apple earplugs