Spencer,
Have you set min and max processor performance to 100% in POWER OPTIONS.
Have you tried turning OFF CPU smart stepping in the bios (or what ever they are calling it this week. e.g smart response technology) ? I see you have an I5 @ 4.4Ghz. Just as a test try no overclocking.
Michael
 

Happens with or without overclock. CPU power options already set at 100% for both min and max. No memory issues. Full re-install didn't help. I don't have smart response installed. Also tried enabling the administrator account, same problem in there.

Hmm. Installed windows on another hard drive, installed nothing at all except my saffire drivers and X3, faders still made noise. Damnit. Something must be wrong with my system then. But what? How can only the audio be problematic. It would help if support could get back to me at last, there can't be 36 ways that noise can come out of fader operation, surely they could help me pinpoint the issue.

Spencer
Hmm. Installed windows on another hard drive, installed nothing at all except my saffire drivers and X3, faders still made noise. Damnit. Something must be wrong with my system then. But what? How can only the audio be problematic. It would help if support could get back to me at last, there can't be 36 ways that noise can come out of fader operation, surely they could help me pinpoint the issue.

If someone hasn't come to Cakewalk with this problem before, and if it's system-specific, then they have to figure out a problem that's outside of Sonar. I really feel for you, these kinds of things are a major hassle to try and track down (I speak from, unfortunately, lots of experience wrestling with computers and software of all kinds).
 
I can't remember if you tried uninstalling the audio interface drivers and using only the internal sound card but if not, I'd try that next. But it still "smells" like something related to video.
 
I keep checking out this thread hoping that you've found an answer I could add it to my "internal database" in case something like this happened to me in the future. Really sorry to hear you're having these issues. Good luck!!

Hmm again. My WMD Realtek onboard sound constantly makes the same noisy timbre as I get when moving faders with the Saffire, except very loud, and independently of faders*. I don't think that's normal, the sound comes out ok on soundcloud, youtube and such. It's beginning to smell like a fried motherboard circuit to me. Noooo, my trusty old mobo :( well, yeah, maybe not so trusty after all.
 
*Nevermind this, after further testing, this was only because of a too short buffer size in the driver settings. With a longer buffer, the problem is the same as with the other cards.
 
I wonder if it could be power supply, or even power bar related, though. In any case, it's settled. I'm selling out, and making cheesy, atrocious pop. Then I'll be rich and when these issues come up I'll just go get a whole damn new setup. HA!

 
This always brings up the point that thousands of people are out there using average quality gear running Sonar with no issues. 
You have a 1 in a thousand issue. And even though like all, you try and blame the software, this is almost never the case. User error or hardware gone sour. 
And yes Video card drivers are well known to cause issues with Sonar. Just like on board audio card drivers, yes Sonar is the most picky of all known DAW's when it comes to the system it runs on, but as I say, thousands of people have no real show stopping problems.  
 
But this does not sound like a software issue to me.

I figured out a way to record the noise, this time from my Focusrite instead of my X-Fi, using the loop back input. http://bit.ly/1h1Sc71
Pretty much the same thing. Support is now on the case. Pause-Break key disables the video engine, and it doesn't solve the problem, so this confirms it's not the video card, from what I understand. I've tested with some spare RAM I have without any luck, and my CPU passes 8 hours of prime95 without errors, so by now I'm pretty much looking for a new mobo.

That noise sound vaguely familiar, I have this Sound Blaster card and when you wore headphones you could hear the mouse when it moved around. And there was always that sort of clock work ticking too. Different , but very close to what you hear. It's interesting how the clicks are at a tempo? 
 
Have you ever disabled your on board audio card during your troubleshooting?  
 
 

yeah it used to be disabled in the bios at first when the issue came up. also, when I put a new windows on another partition, I installed nothing at all, no drivers, no windows updates nothing, except the saffire and sonar, and faders still were noisy. this is when I started realizing that it's likely not software related after all.
 
also like I said I can filter out the noise with a high pass, which pretty much certifies it's part of the signal flow somewhere, thought not necessarily the software itself's fault.
 
oh, that rhythmic click is just the 808 attack, these things sound pretty bad without further processing. heh. click/pops aren't constant and there didn't seem to be any during that recording pass. only the glitchy digital noise from the volume, then pan, then gain faders.

I am TRULY grasping here - what kind of power supply wattage does this computer have?
 
Bob Bone