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I am getting a 2 seconds long beep sound on my XL twise a day. It doesn't indicate anything in phone, just a beep sound for two seconds. It comes anytime.
I don't know if it's some kind of Xperia feature or a problem.
That sounds quite strange!
Have you pulled down the status bar to see if the phone notify for anything?
If you don't have any notifications I suggest that you start your phone in safe mode to see if the beep still appear:
http://talk.sonymobile.com/t5/FAQ/How-to-boot-your-phone-into-safe-mode/m-p/348008#U348008
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Strange. Restart your device by press and hold the power button and volume up at the same time until the device vibrates and see if the behavior comes back.