Lastly, playback a project that you know will drop out. Watch the Performance Meter on the control bar in Sonar. Does the Drive turn Red? Do the Processor Meters peg? Any info in that little box that will point us in the right direction?
 
What Bit Depth and Sample Rates are you using for your project? If you are using a quad rate, try a double (192-96) or if your are using a double, try a single (96-48) something like that. Maybe your drive is having trouble getting all the data into Sonar.
 
Also, be aware that when comping, Sonar tries to read ALL the data for all the comp tracks. If you're like me and can take 200 passes on the same jam, you might try archiving the track and creating a new one after a while so that you can keep all your passes without having to read all that data all the time.
 

For grins, move your entire project to another drive.
 
Last week I was getting dropouts galore.
 
Discovered my projects hard drive was on it's last leg.
 

I tried most of the things you suggested except the USB changes.  For some reason the USB 3.0 on this computer does not work with any devices I have, so I simply do not use it.  Everything else is on USB 2.0 and virtually every USB I have is being used for a device.  The Yamaha keyboard that I use as a controller is included.  I am surprised with the page faults being completely maxed out on that latency monitor s/w that that wasnt the issue... not that I'd know what to do about it if it was but, but I was surprised.  All of the other indicators were really low but that one was off the map.  I did notice that the record bit depth was at 16, so I changed it to 24 as you suggested.  No changes in crackle and drop outs. 
 
Curiously today as I was recording I was moving midi notes in the midi editor and I could even hear crackles on that as well.  Never heard that before with the other interface, even one note at a time, and with only one instrument on the whole project.  After I rendered it and played it on the media player it sounded flawless.  So this in completely a Sonar problem...  The performance bars in Sonar HD is probably at 35% and the other one is about 5%
 
I got distracted and started writing a song... somehow I feel like I only write when Im supposed to be doing something else... Again I really appreciate your help.   Tomorrow when I get home from work I'll start a project from the desktop to see if the HD is problematic, and I'll unplug my wireless internet device and see if that helps.  Starting to look like Ive got to go back to Pro Tools booo 
R

After making the changes noted above, this evening I unplugged my wireless device and it made no difference whatsoever.  I was going to move the project file to another drive as suggested as well, but the project files are by default on the C drive with the program, not sure its going to get any better than that.
 
Q:  What Bit Depth and Sample Rates are you using for your project?
Sample rate is 44.1, which is all that is available in the Asio Panel for the UA Apollo
Bit depth is greyed out and a box next to it is checked as "64 bit double precision"
 
Regarding comping... I am probably an army of one on this opinion but I dont care much for the comping function, so I dont use it very often.  This particular track was a project that was recorded using the old interface.  So I exported literally every track to wav files, built an entirely new project and important all of the individual wav files back into the new project one at a time.  It didnt help... it still crackles like Rice Crispies and has drop outs to the tune of about one every 2-3 seconds.
 
Gentlement once again I really appreciate your time and trouble.   Not having much hope here... the tech support for Sonar said to go through the Windows optimization thing but I did that when I first got the computer.  I think its safe to say that I just spent $2000 on an interface I cant use... NOT a happy camper but thanks for trying

rcalligan
After making the changes noted above, this evening I unplugged my wireless device and it made no difference whatsoever.  I was going to move the project file to another drive as suggested as well, but the project files are by default on the C drive with the program, not sure its going to get any better than that.

Uhhhhhhhh every DAW builder suggests that projects go on their own hard drive.
 
Just curious why you don't do that?

I back them up there but I had a USB drive that completely went south and took about a years worth of work once so Ive never used USB drives for anything but backup since

bapu

rcalligan
After making the changes noted above, this evening I unplugged my wireless device and it made no difference whatsoever.  I was going to move the project file to another drive as suggested as well, but the project files are by default on the C drive with the program, not sure its going to get any better than that.

Uhhhhhhhh every DAW builder suggests that projects go on their own hard drive.

 
Yeah right, that is serious DAW 101! The OP should have at least a dedicated audio drive. I bet that would solve the audio dropouts! You should only have your OS and apps on the "C" drive. Personally, I have (5) HD's in my DAW rig (not counting any external (USB/FW) HD's I may hookup. I have a (2) dedicated "Audio" HD drives (where I can record my waves files to), a dedicated "Project" HD where I store my projects to, a dedicated "Samples" HD where I store all of my samples (100GB of loops, 100+GB of samples from Komplete 10, EZD drum kit samples, etc...), a dedicated "B/U" HD etc....I try to use SSD's (where I can afford it, especially for the "C" and "Samples" drives), otherewise I use high grade 7200 RPM. I am rather shocked that the OP has a "brand new 12 core i7/ 64 Gigs of ram" system for DAW use, but no dedicated HD's (audio, samples, projects, etc...). I just assumed.............
 
Cheers,
 
Billy Buck

You don't need a dedicated hard drive although it is very much recommended (and I agree it's probably an oversight not to have at least one extra drive to store data), a dedicated partition will do. At the very least get the defragger out.

Please make sure you are on the latest driver updates and firmware for everything.

Also please consider turning off Intel speedstep in BIOS or AMD equivalent if your motherboard is one of those. If you are running an Intel motherboard run Intel driver update...

Ta

Did the OP try adjusting his Max Thread Count? It was the first suggestion and I never saw feedback. I had some similar issues on my 8-core i7 with the Apollo 16. I went through tip after tip trying to fix inexplicable audio stutters with no luck. Last night I changed my thread count from 0 (all the cores) to 6. So far it has helped fix the problem. No issues to report.