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I suggest that you test using another pair of headphones to see if you can replicate the problem.
But it sounds like the phone looses connection with your headphones. That is why the music pauses, it should do that.
Anyhow, if it is a problem with the phone or the stock headphones it still needs to be fixed so I suggest that you contact your local support team to get it repaired.
http://www.sonymobile.com/global-en/support/contact-us/contact-info/
In that case its probably related to the phone but exactly what may be the issue is hard to say. Since you have already tried a master reset and a software repair I suggest that you contact your local support team to have this fixed at at repair center.