Sound isn't good

Hello,

Last week I had to replace my harddive and I have spent the better part of the week reloading all my programs, games and such. We play Call of Duty 4 Modern Warfare and the sound used to be great but not now. we have a Logitech X-540 5.1 stereo system and the sound cuts out all the time when playing.

I hooked everything back up to the computer which is almost fool proof since it is color coded but when I test the system I only get sound out of left and right speakers. When playing a game the action usually causes the sound to cut out.

Any ideas on how to fix this issue?