I had this exact same problem! I thought it was dodgy ariel cable (it was running under a door and had been squashed), and replacing that seemed to do it.
Or if not, it could be how my cards were arranged. Is it a new system and a new hardware configuration, or has it just happened. I also have my audio in going into the Mic port on my sound card, cos the line in is also the rear speakers!
My sound card is the C-Media 8738 4 channel card, so it's not a VIA/SB thing. Only thing i can think of is drivers or moving hardware round.
Just for reference, my setup is as follows:
AGP -> Creative GF2MX
PCI1 ->
PCI2 ->
PCI3 -> Realtek 8139 based Nic
PCI4 -> C-Media 8738 Sound Card
PCI5 -> Hauppauge WinTV Primio card
Previously (on old motherboard when i had issues) the sound and TV card were the other way round. Also, before you try changing it all round, get the (IIRC) HCWClear.exe from the Hauppauge website (clears all registry details/drivers)
I didn't try turning off Seti at all, and it would start after using the TV card for about 10-20 minutes.
ConfusedBW