Any idea how to stop this, it's messing just about everything I'm recording. Even when I put the focusrite going into the vs through adat I'm getting the same pops and clicks, some of them even sound like the recording skipped.

I've noticed in the "resource monitor" that there is something called "System Interrupts" and it is at the top sometimes as high as 9 on the CPU while Sonar maxes out at 4 The description of System Interrupts is "Deferred Procedure Calls and Interrupt Service Routines"

I've unhooked the VS700R, recorded though the focusrite into Sonar and pops and clicks are gone, but now I have no control over the software from the VS as it is off. It seems to be in the VS somewhere.

What are your computer system specs ?
Are you recording on to a second hard drive ?
How many tracks are you recording at once ?
Is the computer connected to the internet ?

All of the above can play a huge factor in the way your system runs

Sonar X1D; AMD Phenom II 1055T Processor 2.81GHz; 8GB RAM; 64 Bit OS; Windows 7 Pro; Not recording to a 2nd drive. It doesn't matter if i record 1 track at a time or 12 tracks and I'm not connected to the internet. After the last test without the VS, I'm wondering if it's a driver issue.

Are you using the Asio Driver ?
Try changing your buffer settings.
Have you ran a DPC
http://www.thesycon.de/deu/latency_check.shtml

I agree with Norie.  This sounds like a DPC (deferred procedure call) issue.  Go to the link in Norrie's post and download the DPC latency checker.  Then run the DPC latency checker while you play back audio in Sonar and look at the DPC graph.  If you see red or yellow bars, you know this is the issue.  There is another free application that is helpful in pinpointing the cause of the DPC latency called Latency Mon:

http://www.resplendence.com/latencymon

Thanks guys, I actually used those with my dj software. Anyhow, I played a song through 3 time, did a few fader moves some miner tweaks as the song played and the most I got was 420 @ Absolute Maximum. For the most part it would stick right around 50 in the Current Latency. This 420 was while I had the internet on as well so it would be lower with that off.