I used to have the "exact" same problem on my 2010MP.
Back in the days i contacted Apple about this but they never came up with a solution or reason why these pops were occurring. I never had them on my other computers whom where connected with the same amp/ speakers.
Like others said before i just learned to live with it after a while....but yeah, it sucks/frustrates when a (back then) 5000 computer was having these non solvable issues whilst a 420$ Dell was having no issues with sound at all....