Just saying out loud...not to be a pest or Razz you to madness....
Remember things do not last forever, that Humans Make these days,...older stuff used well has a life span....Some of this new soldering technique used in modern gear, is in my opinion weakly done in ovens these days or rivers Just enough to stick the part on by robots, and when heated over time and time of use for long periods, soldered points can become loose or unsoldered at points of extreme heat build up...and may last 3-5 years...could go longer, but...that depends on a lot of things being put into place properly and maintained and cooled, some Asus capacitors for CPU on older boards I have had, can go bad and start leaking around cpu and onboard video card chips and such!...and certainly to help keep out the nasties of power supplied in smooth sine wave or good power bar, or back up to reduce spikes on electrical can increase life expectancy of the gear, upgraded from time to time....and the old stuff is nice, but has a life span....If nothing has changed....then it is time to rethink a new machine/audio device....Perhaps? as a legacy device is being used on a pci bus...it means you are a bit old in the usage of that system, and things do not last forever humans make these days........Perhaps is a direction one might ponder?

Now asking questions, but looking into other thoughts I posted above...when you tax the cpu it seems to do odd things at this point, and reducing that stress reduces the oddity....So is your cpu toasting slowly with the work load you are asking it to do, and have done over time much with....I see you have some tunes posted up....Nice, and many......see what I mean?...we could trouble shoot this to the end of time....and never get it solved, if it is just a old system dying slowly....if we do not take all info in correctly, and get all info posted correctly to service this,....assumption are taken at times liberally....could be your cpu is on the way out of processing due to extreme heat or ware, or use, or age, or just not capable to run X3e and plugs you want to use, at this time line of time, with what you have?....could be?.....But let us get more info...and see....Buffer settings, irq shared states if any...and then...checking the logs...event viewer views...so on and so forth...dcp checker....and such ...run or looked into...and there are a lot of people here...that know what errors to look for in that process.
 
Regards.

OK, so I've gone through all the posts (thank you!!) and here's what I've found:
 
No updates to video driver or OS, other than any automatic Windows updates.
 
It is indeed X3e.
 
Defrag happens automatically every week.
 
The audio interface is just listed as M-Audio Delta Audiophile. In the Sound dialog it lists S/PDIF, Line 1/2, and Multichannel. Line 1/2 is what I have selected as default. (I have no idea what any of those mean.)
 
As for the buffer sizes, I've changed them up and down everywhere between 64 and 2048, and no change has ever made any difference (to playback). That's in Sonar. The audio driver's interface is external to Sonar, and the ASIO/WDM buffer size is set at 256. Any other setting either higher or lower and the crackles get much, much worse.
 
As for the IRQ settings, M-Audio Delta Audiophile is at IRQ 16, which is shared with Intel ICH10 Family PCI Express Root Port 6 - 3A4A as well as Intel ICH10 Family USB Universal Host Controller - 3A37. At the bottom of this post is the System Summary from msinfo32.
 
I can ponder the outdated-ness of my gear, but before I bought a new system I would probably re-install Windows and start from scratch to see if things clear up. The idea of buying a new workstation makes me both giddy (new techie toy!) and depressed (re-installation and the inevitable Thing That Doesn't Work As Well As It Used To)
 
msinfo32 summary page:
 
OS Name Microsoft Windows 7 Home Premium
Version 6.1.7601 Service Pack 1 Build 7601
Other OS Description Not Available
OS Manufacturer Microsoft Corporation
System Name JIMOFFICE-PC
System Manufacturer ASUSTeK Computer INC.
System Model CM5571
System Type x64-based PC
Processor Pentium(R) Dual-Core CPU E5400 @ 2.70GHz, 2700 Mhz, 2 Core(s), 2 Logical Processor(s)
BIOS Version/Date American Megatrends Inc. 0221, 11/3/2009
SMBIOS Version 2.5
Windows Directory C:\Windows
System Directory C:\Windows\system32
Boot Device \Device\HarddiskVolume2
Locale United States
Hardware Abstraction Layer Version = "6.1.7601.17514"
User Name JimOffice-PC\Jim Office
Time Zone Pacific Standard Time
Installed Physical Memory (RAM) 6.00 GB
Total Physical Memory 5.75 GB
Available Physical Memory 1.59 GB
Total Virtual Memory 11.5 GB
Available Virtual Memory 5.17 GB
Page File Space 5.75 GB
Page File C:\pagefile.sys

You could try reinstalling the interface drivers and see what happens.
 
Also, pop open task manager and see if anything else is running. 
 
Run the DPC Latency checker and see what kind of results you get.
 
The last time I had a slow down like that in coincided with upgrading my video card and once I did I got an unusually large speed boost in my performance. 
 
You may want to run some disk checking tools too, just in case something is getting ready to fail. Sometimes they really do crash gradually, hopefully long enough to do a good backup! :-)
 

could ram failure or unseating of sticks/dust cause this?  Also, I had lots of problems which began occurring from sketchy powerline which, even with a stabilizer/UPS, disappeared once I ran a new line... just reaching here...

One more possibility: disks getting too full?  Even defragmented, that can impact performance.  Just an idea...

Sounds like its your audio card buffer is too low.
 
You need to change the buffer on your audio card not sonar.  To do this go into your audio card software and change the buffer to 2048 then go into sonar and under the preferences menu click apply on the audio driver and it will pick up the sound cards buffer.  Then it should work fine

Is this a laptop or desktop? My laptop is terrible even with the largest buffers and best audio interfaces when on power saving mode. When on "performance" mode (manually tweaking everything for maximum performance) it's a real workhorse.

I see someone's already mentioned DPC Latency Checker, which will tell you if you have a DPC latency problem, but not much else.
 
Far more use is LatenceyMon, which will attempt to work out what the cause is. Download that from here:
 
http://www.resplendence.com/latencymon

If increasing the buffer size to 2048 doesn't change anything, DPC latency may indeed be your problem. You can experience this symptom even though the CPU meter shows low numbers.
 
"DPC latency" refers to the system overhead incurred by processing hardware interrupts. Every adapter (video, audio, disk, network, USB) in the box generates a hardware interrupt whenever data is transferred to or from it. These interrupt handlers run at an elevated priority, so they take precedence over everything else.
 
Sometimes, an adapter or its driver gets greedy and takes an inordinate amount of CPU time, time that's taken away from other adapters and processes. The result is that data transfers to your audio interface can't be processed fast enough and you get interruptions in the data stream that manifest themselves as clicks and pops.
 
Why wasn't this a problem six months ago? It's because something has changed. It could have happened without your knowledge in a Windows Update, it could have been new software you've installed, a plugin update, or even some setting change that you'd never suspect would impact audio performance.
 
So your first step is to either confirm or eliminate DPC latency as the root of your problem. The LatencyMon tool suggested above will at least offer some clues, and if you're lucky it'll definitively point out the culprit. Be sure to read the informative tutorial they've posted at that link. It might seem mind-numblingly technical on the first pass, but it's good stuff to know about.