I'm running windows vista and I noticed I can't hear any guns or missile sound effects in prophecy or secret ops. I also noticed I can't hear some speech, such as when I ask wingmen to form on my wing or taunt an enemy.
Partial-sound issues are fairly rare in Windows WC games. Some easy things to try would be to adjust to different compatibility modes or try different size installations. Enabling options like Full Duplex Mode or Direct Sound Safe Mode for your sound hardware could also help. You should post your hardware details to see if anyone with the same equipment has similar issues.