Hi,
 
I just wanted to share my experience with this issue as I've seen it posted with a myriad of causes and can be very difficult to resolve trial and error.  I was running Sonar 8, passed on the upgrade to X1, then X2 came out and I decided to get the upgrade.  In the middle of all of this my motherboard went down, so I decided to go AMD and got the FX-4100.  Then my video card went out, so I got an Asus HD 5450.  I was about to come to the conclusion that the FX-4100 was underpowered until I looked up the benchmarks for the recommended minimum systems to run X3.  I'm sure I'll run up against 4100's limitations soon enough, but it's nice to know that it'll suffice while I'm coming up to speed.
 
Long story short, the Asus video card loads up a program called GPU Tweak and it caused 100% of the problem.  I uninstalled it, and reinstalled my audio drivers and everything is good.  While I was at it, I upgraded to X3 so I've got a lot to catch up on.
 

Glad you got it sorted. I just love a happy ending...

Asus apps seem to be universally bad for audio. Asus Ai Suite (motherboard utility s/ware) also causes crackles in audio. I had a similar experience to you tracking down the problem. Removing it fixed the problem completely. You could see the DPC glitches go away as soon as Ai Suite was removed.

Hmm, I have Gigabyte system/sound card. If I alter for example one of the Nomad applications, I get audio cut out...hope X3C gonna sort this out?

Thanks Tom. It seems that the major offenders on the pc components are the mother board, video,  and network cards.  Network cards are disabled by many as a contingency, but video and mother board are driver/hardware tricky. 
Thanks again. 

I have an ASUS P9X79 PRO motherboard with the AI Suite installed. I'm running Win 8.1 without any issues at the moment. I'm even overclocking by 36% at the moment. I'll keep an eye on it.

Good to know. thanks

cconde
Thanks Tom. It seems that the major offenders on the pc components are the mother board, video,  and network cards.  Network cards are disabled by many as a contingency, but video and mother board are driver/hardware tricky. 
Thanks again. 

In the case of the Asus stuff, it's not the components or even their drivers per se, but the utilities that are bundled with the install disks.

mudgel
I have an ASUS P9X79 PRO motherboard with the AI Suite installed. I'm running Win 8.1 without any issues at the moment. I'm even overclocking by 36% at the moment. I'll keep an eye on it.

When I was tracking down my problem, I ran DPC Latency Checker.  I would get lots of DPCs when Ai Suite was running.  If I then right-clicked on the AI Suite icon in the system tray and exited out of it, high DPC latency would go away completely.  The worrying thing is that some of those glitches were being recorded!
 
I could obviously hear the problem, which is what led me to seek a solution, but it would be worth monitoring your DPC Latency to see if it's causing you a problem.

thank you... no asus then ;) (i used to have an asus laptop back then...)