Get close to the hard drive on your computer and the monitors at the same time and see if the pops coincide with the hard drive working. You may have to launch a program to hear it. I've heard this when using my built in soundcard instead of my Delta1010.
I doubt it's damaging the speakers.
You may need to get better cable to connect your monitors to your soundcard, but you didn't mention any other gear, or how you're hooked up, so I hesitate to make any suggestions on how to fix this.
Does it go away when the computer is shut down?