OK - tried testing on my laptop - unfortunately that is USB3 as well, but it does behave exactly the same way.
So this at least proves there isn't a specific problem with my installation - and the problem appears to be re-producible.
I tried installing the jBridge demo on my primary DAW, and that appears to overcome the issues. I've tested a number of the VSTs that will not play, and their 'jBridge versions' will play without problems.
 
So I'm thinking this is now some kind of incompatibility between the Focusrite drivers and the Sonar BitBridge software. (It may also be linked to USB3, but without a USB2 device, it's hard to confirm). I'm not really sure how I move this forward - I don't know if I should try and report this to Sonar/Cakewalk, or continue pursuing support with Focusrite?
I may consider purchasing jBridge, but to me this seems more of a 'workaround' rather than a 'solution'...
 
Does anyone know if there are any 'freeware' alternatives to jBridge / BitBridge?

Just a quick update - I've done a clean re-install of Windows 10 and Sonar X3
I'm still getting issues with 32bit VSTs - and now the three 32bit VSTs that come with Sonar (Cakewalk Sound Centre, DropZone and rgcAudio Square I) are all now exhibiting problems - which at least makes the issue consistent!
I've had a response from Focusrite - they agree it could be an issues with the Sonar 32bit wrapper (BitBridge) - but they are not fully staffed until the new year so I won't get a full investigation until then.
At the moment I'm hoping I can make do with 64bit VSTs - but may have to look at jBridge if I find I need some of my older VSTs (and Focusrite can't resolve the issue) 

I would file a problem report with Cakewalk if you haven't already.
 
https://www.cakewalk.com/Support/Contact/Problem-Report
 
I would also experiment more with WASAPI and WASAPI Exclusive in the meantime. Windows Audio has been improved in recent months and Sonar has been optimized for it (nevermind, I see you're on X3).
 
I haven't tried any alternatives to jBridge / BitBridge because I (luckily) haven't needed to.
 
EDIT: You might even want to try your integrated audio as a temporary work around.

On my laptop I have exactly the same problems (HP laptop i5, Windows 10 and Focusrite Scarlett Solo 2nd Gen). Also in my case the clicking and crackle only appears with 32-bit plugins running over Sonar's BitBridge (No problem with 64-bit plugins). It makes no change whether I use an USB2 or USB3 port. When I test the same old plugins in a 32-bit DAW (MAGIX) on the same system, they run without any problems. This proves that the audio interface setting is generally alright.
When I test the 32-bit plugins on my desktop system with a Tascam USB interface in Sonar, there is no problem either.
 
Thus the problem has something to do with the interaction of the Focusrite driver and the Sonar BitBridge. I think the 2 companies should sit together to solve the problem, but as I worked many years as software engineer myself, I know that this is often a huge problem and so the only one who will be blamed is the end costumer, unfortunately!
 
I have contacted the Cakewalk support some days ago, before I have seen this thread. The only reaction of them is that they sent me twice a general e-mail with advice to check the settings of my audio interface and of Windows 10. That helped nothing at all!

Thanks Marled -Although I'm sorry to hear you're having problems, I am pleased to hear the problems exist on another setup.
I have a call open with Focusrite about this, but their response so far has been similarly 'generic'....

The same problem happens to me with 32bit VST plugins (... and among them the nice Pianissimo VST that I use often):
 
My PC: Windows 7 64bit, Intel i7, USB3 (all ports), 16GB RAM, FocusRite Scarlett 2i2 2nd generation
 
I tried to change the ASIO buffer, but the problem of a repeated tick (while playing and while recording) is still there.
 
No problems if the plugins are used with other hosts (e.g. savihost).
 
 

Hi,
Focusrite support have confirmed this as a bug:
 
 
 
Hi Paul,

Thanks for your reply,

Apologies for the delay in response. I've managed to test this with Sonar and I have managed to reproduce the problems you are having on 4.15 with Sonar.

I'll log this as a bug case and add you to the case.

During initial testing I could not reproduce this on the 4.14 driver so I would recommend installing this and let me know how this goes. 

I've also CC'd myself to this thread so I'll be notified when you reply.
Best Regards,
Ed Fry
Focusrite Technical Support

I had also contacted Focusrite and after some mail ping-pongs (their response time is about 5 days) I wrote them about their bug report above, so they sent me also the 4.14 driver. And indeed, my problems with noise using 32-bit plugins has disappeared with this older driver!
 
(Sonar Platinum, Focusrite Scarlett Solo 2nd Gen)

Just wondering if the Splat 2017.01 update might of addressed this. I will have to try on my set up later.
 

jadonx
Just wondering if the Splat 2017.01 update might of addressed this. I will have to try on my set up later.
 

Hi. Reading this thread, it seems to have been a Focusrite bug, and not a SONAR bug. Do you have the 4.14 driver for your Focusrite mentioned earlier?
All the best.