Is this a recent build or it just started one day? What OS are you using (did you perhaps just move to win8)? I can only say check your connection, make sure drivers are current. Not to sound wise but, why not just leave your sound card in the top slot then?
The drivers are all up to date so i don't think it's that. The reason i want to fix this problem is because i bought a game capture card and when i connect an audio passthrough to it, it causes the audio to crackle and whine because it's in a different PCI slot.