What is wrong with the system sounds on my laptop?

I know that questions like this usually become orphans, but here goes:

I have a Sony VAIO CA computer. The system sounds are messed up. Yes, I can hear them. Yes, it is the right sound that plays, such as the “click” sound when you click on a folder or the “ding” sound when a dialog box opens up asking if you want to “save changes” or something. But what happens is that the sounds are often muffled and shortly after that I hear a “pop” sound in my headphones. It happens with the speakers as well.

No other sound seems to be messed up. Listening to music is fine, playing videos online is fine, etc. It’s just the system sounds. What is going on?