The projects were brand new projects I created in X3.  This one in particular was playing fine, and then it wasn't.  Also, brand new install of Play with the latest version.  
 
Yes I am connected to the internet, and do have virus programs running (although not scanning).  So for example, I might go back and forth while watching a video on Groove 3 while working on a project.
 
I'm definitely going to try replacing the instances, when I get home.

I don't think you  responded to my earlier request, or if you did I missed it - did you try upping your Prepare Using nnn Milliseconds value from the default of 250, to 500 or even 750?  It is in Edit>Preferences>MIDI>Playback and Recording, if memory serves.
 
Bob Bone
 

Sorry I must have missed that, I will try that tonight as well, ty.   Though it's strange that when I recreated the project, the crackling went away. 
 

I am reaching - so it may not even apply, BUT some folks definitely find the new default of 250 milliseconds too small, and bump it back up to either 500 or 750 ms and their problems vanish, so I thought it worth a try.
 
It does sound like some issue local to your computer, as the other poster seems to be happily not having the same kinds of problems you are, so maybe recreation is the ticket - I am just out of notions.  :)
 
Bob Bone
 

Kroneborge
Sorry I must have missed that, I will try that tonight as well, ty.   Though it's strange that when I recreated the project, the crackling went away. 
 

 
This may or may not be relevant but for some time now I've been convinced that Sonar projects can take on board various aspects of weirdness and corruption the longer you work on them, especially when there's a lot of VSTi's involved. I've had to recreate a number of projects over the last couple of years for reasons which included bizarre behavior from ProChannel modules, Native Instruments synths & effects zeroing their settings on playback, various track editing weirdness, crashes and dropouts. I've had the occasional vague suspicion as to the causes - turning synths on and off in the synth rack, using the "replace synth" function, toggling the interleave on simple instrument tracks etc. Nothing definite enough to have been able to file solid bug reports of course, but I have had a couple of projects off to the Bakers for observation. 
 

I tried adjusting the intel speedstep, and also the midi buffer, didn't help.  I replaced the synths with the EXACT same synths, playing the same part, fixed....
 
I think for now, I will just chalk this up to something weird getting corrupted, unless I can get something repeatable.
 
I will report back if I start getting problems on other projects, thanks again for all the help and ideas.
 
 

Hey - I am just glad you got past it.
 
Bob Bone
 

Just a simple question:
 
did you set up the power scheme in control panel as "HIGH PERFORMANCE"?
 
I noticed that sometimes and in some situations, this could be a problem, if the power scheme is not set as I mentioned.
 
Regards,
 
Giorgio

I let this drop for a little bit, cause frankly I didn't want to spend anymore time on it, but I started a brand new track and still having problems.
 
So for example, I open a new project, install ONE vst (FX Expansion tremor).  I've got a simple drum loop going, and then all of a sudden audio stops.  if I open up the preferences menu, and then close it again, I will get that reverb popping sound and then sound starts again.
 
Note, I was not watching video's or doing anything else, just happened to be renaming a track.   So far I haven't noticed enough of a pattern to make this repeatable or not, but it's happened more than once and extremly frustrating.
 
I'm not sure what else to do...

This has resolved weirdness like this for more than one occasion with my Saffire.
 
Take a screenshot of mix control.
Uninstall mix control.
Reboot
Install mix control 1.8
On mix control restore factory default.
Set up mix control manually using screenshot as reference.
 
If that doesn't work (there's a good chance it will) you might try contacting Focusrite.
 
Cheers...