Do you have onboard sound? If so...thats probably why....if its not a great motherboard and usually even in somewhat newer boards...onboard sound sucks. The reason it skips during games is because its using up your CPU AND trying to send the sound through the soundcard...so its basically 'lagged' if you will. Same thing would happen to me while playing Command and Conquer: Generals so I popped in a spare sound card and it fixed that problem right away. Get a cheap soundcard if you can. Thats my only suggestion
I had a similiar problem just recently. The cause was because I connected the USB header incorrectly to the motherboard and/ or I had the CPU overclocked. Check your USB connections, if you do not know if they are connected properly to the correct pins on the mobo have someone knowledgable check them for you tell us how you did it. Did you overclock memory or processor?
Still man..I'm telling you...its just cause its onboard =/ I Hate to tell you that but, it's the truth. I have an MSI KT6V board with 5.1 surround sound option too...its cause you're computer is struggling with the game and trying to produce the sound too. You'd think 'well doesn't it have to do that anyway on a PCI Sound card?' yeah probably...but the architecture of a sound card will be more complex than one built into a motherboard. gotta consider all the other signals and voltages running through your mobo. Not sure if you can do anything about it =/
I had a similar problem with onboard sound. I installed all of the newest drivers and everything but it still didn't work. Like Nubius said you have to get a pci sound card. As soon as I installed it the sound in all of my games started working fine. Plus buying a 5.1 sound card isn't that expensive.
Yeah...its a nice concept and all to have onboard 5.1 but I think they just haven't worked it out good enough to the point where your system CPU, RAM, and GPU are being taxes that it can put out that good clean sound