I am having the exact same problem. Happens with TF2 as well. What is your audio source ? I am using the Envy24 Family Audio Controller from VIA (on board my motherboard, Gigabyte G31M-S2L). According to the Gigabyte website, it uses the Realtek ALC662 codec.
Do you also use voice communication in game ? Or outside like with ventrilo ? I am wondering if that has anything to do with it.