I just started having the same problem after installing Windows Server 2008 R2.
The Motherboard is a Asus P5E WS Professional.
Tried 2 sets of speakers, and they both do the same thing.
Had to download drivers for the Realtek soundcard from CNET, because nothing from AUSU would install on Server 2008.
Powering down the machine completely then booting up the problem was gone.