Another possibility is plugins. I find, as much as I like Izotope Ozone 5, there are a few settings, particularly in dynamics and volume maximizer modules that cause a lot of pops and clicks (they're higher resolution and need more ticks). The same goes for some VSTs like U-He Diva...it sounds great, but man, at the higher resolution audio settings, ...ssssst-t-t-t-uuuuu-tttt-t-t-te-rrr-r-r-rrr....
 

why SONAR would not be able to query it's own initialization file to get the desired buffer settings without having to force a change in the INI files.
 
IS NULLABLE (programmers out there)...

That is all :)
Just a theory... probably just my stupid theory....

Neirbod,
 
One more thing to consider in case you haven't run down the problem yet...
 
Are you doing anything with your interface that might cause the problem? For example, is your interface output gain above 100% or are your routing multiple outs to the same master? That can be hard to find b/c it isn't actually happening in Sonar and could cause clipping.
 
Sometimes my external sends end up routed to my master outs and when I audition I hear clipping b/c they are mixed in with the masters. If I bounce to tracks and select the master bus, I don't have the problem because the extra summing only happens at the interface where the sends are summed with the master bus and sent to the master outs. The Master Bus isn't clipping... the master outs on the interface are because the external sends are being summed in again with the Master Outs.
 
So, in Sonar, there is no clipping to find. I would have to see it in the interface software.

I may have missed it - do the crackles go away if you hit 'E' to toggle on/off the Bypass All Effects?
 
Bob Bone
 

Well I stupidly overlooked MIDI playback buffers, now this is sorted I'm rock solid and my latency settings can now be reduced again...

I can only chime in and say that I have basically the same setup and problem as Nirmod - except that I'm running a UCX, instead of UFX. Things have been crystal until X3d so it's quite obvious the boys/girls ****ed up this time. I find it also highly amusing that people recommend checking buses for clipping, make sure they have a TI card, bypassing FX etc.etc when it's obvious things worked flawlessly with the exact same setup as before and the only thing that has changed is the software version. For me the pops come for such small things as activating the audio engine. Horrible. 

JohnRick
I can only chime in and say that I have basically the same setup and problem as Nirmod - except that I'm running a UCX, instead of UFX. Things have been crystal until X3d so it's quite obvious the boys/girls ****ed up this time. I find it also highly amusing that people recommend checking buses for clipping, make sure they have a TI card, bypassing FX etc.etc when it's obvious things worked flawlessly with the exact same setup as before and the only thing that has changed is the software version. For me the pops come for such small things as activating the audio engine. Horrible. 

Glad I highly amuse you.  
 
I asked a question about the bypassing of effects because that HAS caused dropouts and such for other folks in the past, and since I have no idea of what is actually loaded into the problematic project, I thought I would ask - which I also prefaced with an indication that I may have missed other relevant information.  
 
And, checking the results of bypassing the effects and turning them back on is perhaps 1 minute of time - likely less than the time to put your post out there.
 
Lastly, just because an issue is exposed in X3d does not necessarily mean that it is CAUSED by X3d.  It certainly may have been, but there have also been issues with deficient plugin code where it shows up after a particular Sonar update, but is still an issue with the plugin - just uncovered by some slight variation in Sonar.  
 
If I did miss the original poster's explanation of the project at hand having the issue, then I will again apologize - I DO stand by my question about bypassing effects being a reasonable one - the OP could have skipped it if it did not apply.
 
Bob Bone

JohnRick
I find it also highly amusing that people recommend checking buses for clipping, make sure they have a TI card, bypassing FX etc.etc when it's obvious things worked flawlessly with the exact same setup as before and the only thing that has changed is the software version.

Not necessarily - I've had multiple Windows and graphics drivers updates since installing X3. One of the graphics updates (NVidia) was a disaster. Usually I do a rollback and the next update solves whatever problem there might have been but this time I just threw in the towel, got an ATI graphics card recommended by PC Audio Labs (it's fanless, too!!), and it's been smooth sailing ever since.
 
I cannot tell you how many Windows software problems I've had (not just Sonar) because of graphics cards and drivers. I do not have this problem with the Mac...well, except that my Mac can't use its existing graphics card if I want to do the 64-bit hack so I can run Mountain Lion or Hello Kitty or Mavericks or whatever the latest OS is on my desktop...still stuck on Snow Leopard 'cause it works.

CakeAlexS
My issues are resolved! (Famous last words)
I have absolutely no idea why (could still be my PC) but I'm wondering if values are not persisting in Sonars database, or some sort of value corruption. This is totally pie in the sky, not much logic to it, but try this...

Open Sonar, Open a project
Go to Preferences -> Sync and Caching
Take note of play and record buffer size. Double them (or something)
Click OK
Go to Preferences -> Driver Settings.
Click ASIO Panel.
Click OK to close preferences.
Play your project a little.
Close Sonar.
Open Sonar, Open a project.
Go to Preferences -> Sync and Caching
Put ye olde values back into play and record buffer size.
Click OK.
Play project.
Close Sonar.
Stand on one leg.
 
Now is there a now difference of have I sent you on a wild goose chase?
(I suspect people have different scenarios here, however it may help somebody, or maybe it's just my imaginary friend).
 
This post of you and a driver downgrade to the focusrite mix control 2.4 saved my life,
thanks alex

> This post of you and a driver downgrade to the focusrite mix control 2.4 saved my life,
thanks alex
 
! :)
BTW I'm running Mix Control 3.3 fine, are you by any chance running the legacy firewire driver because that is not needed for 3.3. Also with 3.3 I think I had to clear to go to File -> Clear Settings or even File -> Restore factory defaults (a distant memory now).
 
Hope this helps...