jkoseattle
The thing of it is, whatever I'm using video/audio/accessory-wise is the same thing I was using six months ago.

Though this seems to be the most relevant thing, you kind of need to let it go because it only tells you not to try everything to fix it. You have to look at things it can't possibly be. I had a stutter on older projects last week. The now line would update every 1-2 seconds and not run smooth. Couldn't figure it out. My 2 monitors run off the i7 mobo on HDMI and DVI. I switched the HDMI to the main monitor and DVI to no. 2. That fixed it. And that couldn't have been a problem, but... I had a PCI card that had USB's on it and if I put the mouse on that card instead of the mobo all kinds of weird stuff went on. I threw out all PCI cards I had and only use PCIe for more USB or anything. If you have eliminated the possible or probable then only "it can't be that" is left. A wireless mouse of keyboard on a PCI card waiting around for it's turn can be a PIA. Unless  you have not updated Windows or any software your system is no the same as it was. Thinking "it worked on that latency setting before so it can't be that" is not true. So try what these guys are telling you. They are smart, have a lot of experience and want to see it fixed.                   

Min system requirements for X3 is in cpu terms: Intel Core 2 Duo E8200 2.67 GHz
 
I think you are a bit low in that term...E5400.
 
Are you using HD Audo through the video HDMI?..or have it enabled?
 
So here we have a problem, you are below minimum I believe...it might run, and you may have done a lot with it....but you are pushing it with this setup in truth.....Right?...and that means just running sonar...never mind plugs!
 
That Asus system is the low end run....Be mindful...You want good results in computer music production...You should put in some more dosh...as it is a cash cow kind thing....No disrespect, or ill will ...Just my truth found many moons ago!
 
Best wishes....I'll keep you posted if I find more input as I asked for...and try to see if that HD hdmi audio is on, and turn it off.

So no MB Manual of merit for this Motherboard...to seek irq share slots if any, or any nice pictures of it found Yet of the inners of that system, and others are having issues finding also.
 
So a windows System info...is ok...but the IRQ listing is what I want to see...and devices being used...please..
 
If you got internet device on, then turn it off, wi fi, turn it off...and then try again.
 
As I cannot truly see why one would put a below min system spec through the stress test, find problems, and ask what is wrong....When it is appearently the cpu and system is not capable of doing what you want to do with it perfectly as the builders ask for a standard be met first.....And I do not think you have.
 
And 4gb for windows 7 might be fine, but top that with EW which uses plugs to memory...or hardrive, and yet still used cpu loads....might just put that smoking cpu into fits of frantic convolutions...add some plugs ins...and you got problems!....Right?...so you got 6gb...not much difference really.

Perhaps a earlier version, that has no bugs of Sonar, might prove better performance for you with this system spec...?

If you have a backup image more than 6 months old, you could always restore that as a sanity check. (Then load up the project and see if you get the crackles or not)

Just be sure to make a backup image from today so you can get yourself back to where you are now.

I have a Delta66 (not a million on miles different than your audiophile). If I get crackles like that, it's from high CPU usage, and increasing the Delta buffers will fix it. I'm just saying - that's where I'd look.

In a recent post from Craig A he had a similar experience. After much trouble shooting he took the project, made cakewalk bundle file then reopened it. It seems that some times a corruption can creep into audio and project files that once having been through the bundling, de bundling process is then fixed.