I got an external drive hasn't arrived yet.  But I did save a new song file to my desktop and it made no difference whatsoever.  I do seem to remember reading something about a thread count but even though I an fairly tech savvy not sure how to do this.  I am very willing to try this one however...
 
I purchased ProTools but haven't opened it yet... I would love nothing more than to stay with Sonar.

Go to Preferences. Make sure Advanced is selected in the bottom left corner. Select Configuration File from the menu on the left side under Audio. The second row from the top should say MixThreadCount. The default value is 0 which mean as many threads as you have cores available. In your case, 12. Set it to 9 or 10. See what happens.

Here's what UA finally replied with concerning my similar issue...
There are a few things I would recommend off the bat:
Boot Order
First, make sure you are always booting up the system in the following order (this is to make sure the Apollo makes a stable connection to the driver):
Turn on the Apollo first > Then turn on any additional peripherals > Turn on the computer last.
Uninstall / Reinstall
It would also be a good idea to perform an uninstall / reinstall of the UAD software in case the driver wasn't installed properly the first time:

When reinstalling, make sure to use the latest version of UAD software found at the link below:

Buffer Size
When using the Apollo via FireWire we generally recommend working at a buffer size of 512 or higher - you may be able to work at lower buffer sizes without issue depending on the specs of your computer however this is where you should start, and if you don't run into problems experiment with lower buffer sizes from there. A hallmark symptom of working at too low of a buffer size is audio drop outs and other audio artifacts that won't be present in the actual waveforms of your audio. Let me know if the problem persist working at 512 or higher using the two suggestions I mentioned above.
 

One more thing.
 
I did some more experiments using Windows Performance Analyzer. I tried different values for MixThreadCount. 6 seemed to be magic number. The test was run by looping a 15 track song with 1 UAD plugin each and Sonar's ProChannel FX with a buffer of 128.
 
At 0, I had CPU spikes every minute or so.
At 7, it was actually much worse.
At 6, no spikes.
 
It works for some reason.

I will try this tomorrow I have absolutely no idea what I am doing but it is certainly worth a try.  Thank you very much for helping me on this.

OP... did you try the thread setting change yet? Your symptoms sound very similar to the problems I was having with the APOLLO a couple of years ago..... figured this out (not sure why it works) and I was pleased to see that it helped colinTheBrewer as well.
 
My theory in trying this was that "perhaps" there wasn't even cycles left for the OS to do zoom since X3 had them all.... like you said, it works and I don't really know why either.
 
Jim

Sorry its taking me so long to respond work is really busy.  So I finally got a chance to try this.  As luck would have it prior to the trial I couldn't get it to misbehave.  So I started a session and recorded a bunch of tracks, and finally it started.  So I switched it from 0 to 6, and I do believe it corrected the problem... I was really excited and I am grateful for your help on this.  However I must've been doing something else wrong today as my vocal recording right after that was really odd.  I could turn dials all I wanted to but nothing changed the sound.  I had everything cranked up so loud it shouldve blew me out of the room and could barely get an audible recording.  I never  had this problem before....I changed the thread count back to 0 and it made no difference, so I kept it at 6.  I may have to try this again tomorrow.  Thank you again I really appreciate your help.  

Ive now been running for about a week with no crackles.  The thread count thing appears to have solved that problem.  I SO appreciate your help on this. 
 
However sadly this week's problem (note a little sarcasm there...) is latency that is so bad you cannot use the system at all.  I do not think these two problems are related as last week I was recording just fine.  The latency was there but I lowered the buffer size to 256 for recording and it was very tolerable.  However today no dice....  I even tried dropping it to 128 and the latency was like almost a second.  Frankly I am very sorry I bought this thing.  I cant be the only person on the planet that want to work on Windows using Sonar and use a better interface...  any suggestions?

Not sure what would cause that... A full restart may help?
 
I just wanted to add that I was still experiencing some problems even after messing with the thread count parameter. I eventually went into my BIOS settings and disabled hyperthreading. It seems to have helped the stability, but I'm not crazy about having to do that. I'm also replacing my FW800 card with the Sonnet version. Supposedly it's more stable.
 
I'll post my results!