OK guys, this has happened to me. Both using the stock Music player and PowerAmp player. I also noticed when the "clicks" happen the phone screen doesn't light up when pressing the home button. I did as 1st_Paladin says by soft reset, however, the issue returns. This same issue happens when I listen to music while running with my Nike+ app. Anyone seeing a pattern here?
The best advice I can give you guys? Restart your phones daily. Long press home key, and choose Restart NOT Shut Down. Even my ringtones have magically muted! However, after a Restart it returns back to normal volume.
I have a stock ROM as well, and did nothing to my phone.
Can you guys try the RESET before your days starts and confirm if it works best for you?