Not sure if it will damage your speakers, but your computer should not be making noises when you are scrolling or doing other tasks. You should look into getting your computer running a bit more optimally.
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Commcat, not sure I understand your comment (is scrolling a page a task?!). these are not sounds from the OS like the ones it makes when you make a error or close without saving, etc.. these are like scratching noises that will interfere in the sound causing the speakers to distort. the solution in my case is to buy a better PC.
I'm just concerned that all this distortion may have damaged the speakers somehow. is that possible?
I do not know if this is the best advice for you, but whenever I have a strange computer issue that seems to not resolve itself. I will backup all of my important information, and reinstall the operating system. Having a fresh install of an OS could speed up your system and your settings will be at default. If the problem still continues you can change sound cards.
Hope this helps, and remember make at least 2 copies of your backup. Because once you loose your data it is gone.