I have a 13" and a 17" MBP IC2Duo. The 13 has this problem but the 17 does not. I am quite sure that the sound occurs when the sound card wakes back up (which can be annoying during a presentation) because if I set iTunes volume to 0 and leave it playing an endless loop then there is never a popping sound because the card can't sleep while sound is played even if at vol 0. (It is a power saving technique, ingenious when it works right) I have friends with the 13" IC2Duo which all have the same problem. This makes me wonder if the problem is actually with hardware/software incompatibility. BTW The problem still occurs when I use a Behringer U Control UCA202 USB Audio Interface.
This power saving technique has been in Macs for quite sometime and the popping problem has surfaced in previous models. I think that a software fix could help but until Apple decides to do something other than bury their heads in the sand on it nothing will be done about. As for me, I will keep using an endless sound loop to stop the popping.
Hopefully a fix will come soon.
as for me, i Also have the pops when listening to music or watching a movie...so in my case nothing to do with the card waking up from sleep since its activated when watching movies or listening to itunes.
still waiting for the replacement hopefully this one doesn't have the problem but I'm not getting my hopes up.