Lately I have been getting a lot of popping noise from my speakers when certain sounds are produced. I had this problem with a discrete sound card awhile back and took it out... went back to the on-board sound. It is doing it again now with the on-board sound.
I have an Altec Lansing 3-way system from the dark ages that sounds great otherwise.
Sometimes when parts start to fail you can get strange issues like this.
My old Altec Lansing sub ended up doing that(only at certain frequencies) about 8-9 years after I first got it. It was a bit worse because when it would happen the sub would shoot all the way forward(i am sure that was no good for it). Because it was the Select 641's with dual subs, i just connected the sub to the other amp(series so the amp was not loaded heavy) and used it for about another year that way. No parts looked damaged(the mosfets[because it was a pwm amp] almost looked to have had the makers numbers burned off at the factory for some reason) on my set inside, but clearly something had started to go.
To rule out a computer issue, you should try to run it off another source like an mp3 player/phone/dvd player ect. Trying them on another plug is also a good idea.
I know it sucks, but nothing seems to last forever. Those old 641's sounded great.