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After trying all those things and thinking the problem was solved, it started again.
So, I repaired the software from PC Companion again saving a few information: just messages and contacts.
When I turned on the device again, I didn't register in any place so I could go to Settings>Apps and disable the ones I don't use. Then I registered in Google, Facebook and Twitter, but via App not via Xperia. And I have updated none of those apps just in case. Definetely, the sound hasn't appeared again. I'll try to update them to another releases and hope it doesn't happen again.
Anyway, I've tried to erase my profile from myXperia, just in case that's the app that created the problem, and I have found no way to...
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The notification sound that you hear, is it the same sound that you have set as notification sound via Settings > Sound > Notification sound. Or do you have this notification sound for a specific app or similar?
You can always try to boot the phone into safe mode to see if same sound appear:
http://talk.sonymobile.com/t5/FAQ/How-to-boot-your-phone-into-safe-mode/m-p/348008
Okay, well try safe mode for a while and keep us updated.
I've been using the device for half an hour in safe mode. It works perfectly. But when using normal mode again, I could still hear the sound. So I've looked wich apps are working and I've turned off some of the apps that are working in second plane. Also, I've turned off notifications for a lot of apps that I don't use and that are not working in the device in Settings>Personalization>Notifications. And it has worked. I'm not sure wich of the steps has worked but it seems that the problem has been solved or, at least, it has worked for some hours.
Sounds very strange. Another thing I came to think of, do you use any type of case/cover where you can place your credit cards or similar in? If yes, you might want to check that NFC is not marked. You can find NFC via Settings > More... > NFC, in some cases the NFC function tries to read the cards and when it fails (since the cards are encrypted) there will be a short notification sound.
After trying all those things and thinking the problem was solved, it started again.
So, I repaired the software from PC Companion again saving a few information: just messages and contacts.
When I turned on the device again, I didn't register in any place so I could go to Settings>Apps and disable the ones I don't use. Then I registered in Google, Facebook and Twitter, but via App not via Xperia. And I have updated none of those apps just in case. Definetely, the sound hasn't appeared again. I'll try to update them to another releases and hope it doesn't happen again.
Anyway, I've tried to erase my profile from myXperia, just in case that's the app that created the problem, and I have found no way to...