I was experiencing the same random 'pop' sound every few minutes. This was happening on my late 2012 MacBook Air and now my new MacBook Pro after a restore from time machine. Finally, it turned out to be Kaspersky AV. If you are using Kaspersky AV, click the icon in the menu bar, choose preferences. Click 'Additional' next to Events Notification. Under Functional Failure, there is a listing for 'Update Error', balloon is unchecked, but sound is checked. Uncheck sound and the issue goes away.