Beeps, I hate to ask but what are your system specs? It's hard to generate ideas without knowing what you're dealing with.
I use Ccleaner continuously and have found a lot of TSR programs trying to run undetected. Ccleaner lets you experiment with shutting them off in windows. I use SSD's so my machine never defrags. I believe in Win 7 it will try and defrag regular drives in the background. Nothing throws a wrench into the works like disk activity. Try turning off disk buffering in the Sonar settings if it's still active.
 
If your machine specs are good this should be 100% fixable.

Beeps - offline rollback takes less than two minutes. Just run the installer for whichever version you want to use. I have done it a dozen times without issue. The situation you are in is exactly what it is for. 

Yeah, sorry to not be more forthcoming with details at this point guys but I am truly in the middle of a fer realz, pro session so I can't be poking around and whatnot until it's done. I am gathering data points as I go though and keeping an eye on what's doing what.
 
The basic system specs for now (without all the model numbers and the like which I always forget) are...
 
i7 2600k
16GB Corsair Vengeance DDR3
C drive 500GB 7200RPM (programs/OS)
E drive 1TB 7200RPM (audio/general storage/couple of streaming libs not in use in this project)
*note: I have Sonar installed on the C drive but projects and audio are on the E drive
Win7 64bit (up to date)
Interface Focusrite Scarlett 18i6 (USB 2.0)
 
I do not have a wireless card and keep the system offline.
 
I disable my AV when recording.
 
Seriously this only started going wonky after the Lex update. I have gone back to using 96khz on the request of the producer but that's what I usually use for my own stuff without issues.
 
Anyhoo... that's as much extra deets as I can muster for now. I don't think there's gonna be a simple solution to this.
 
Cheers.

I have also noticed a bit of performance change in Lexington. The CPU meters jump more than usual and I have had the occasional click or pop that I have not had to deal with in JP.
 
I usually run with buffers set to 128 but needed to increase to 256.
 
The usual culprit that causes the clicking for me is having the gui for Jamstix open. If it is closed then playback at 128 buffer is glitch free with JP and earlier. With Lexington even with the gui closed I am hearing glitches during playback.    
 
Specs in Sig.

I'm clearly not pushing enough data to see these problems. Did you try the old "disable the 64 bit double precision engine" bit in the audio set up. I've had that turned off since X1 and never turned back. It has shown up as an issue a few times over the years, might as well tick that off the list.

I found the same type of issues with Lexington, basically it seems to use noticeably more CPU/resources, than any past iteration of Sonar that I have experienced. After not using Sonar for some time I updated to Lexington to check it out and noticed issues straight away, started a thread Here marked it as solved, but as I continued with the little project adding more stuff the crackles and pops started returning, it was still only a small project, I had to change my buffer settings dramatically to stop it from occurring, never had to do that before. I can run the same project in Studio One 3 and Reaper without issues and with buffers at 128.
 
I moved the project entirely over to Studio One, it has now grown considerably larger and there is no sign of any issues and no need to alter buffer settings. I have always found Sonar to be seemingly heavier on recourses than needs be compared to other DAW's I use, part of the reasoning to check out Lexington was the optimizations, speed increases etc I had read about, but from what I can see things have gone backwards.
 
Further reinforces that my move to Studio One 3 some months back was a good choice for reasons more than just features. But I keep checking in with Sonar (purchased another 12 months subscription), and I read somewhere that Cakewalk were taking the knife to Sonar and cutting out old inefficient stuff, that can only be good, because I think there is a lot of old inefficient stuff in there going back to the last decade if not century. Clean it out, get rid of all the old inefficient stuff, bring it up to todays standards, I don't care what anyone says about benchmarks against other versions of Sonar or other DAW's, the only benchmark I care about is my personal one, and it says Sonar is behind the 8 ball, and that Lexington has stepped backwards. Lets see what the future brings.

Interesting...  Some things are snappier like the update notes state, but from a pure performance aspect I don't find myself needing to run with higher latencies with Lexington than before.  This on Win7.  Obviously there's something accounting for the difference, but I have to think it's a Lexington+system thing.   I am curious to see how the next update pans out...