Jeffiphone
chuckebaby
jatoth
Are you playing back immediately after recording? What happens if you record then wait a few minutes before playing back? I'm thinking it's video related when Sonar is trying to redraw the wave forms.
Just thinking out loud.
I have a similar feeling. especially seeing how sonar now uses open GL its important to update to the newest version driver and windows update. but im not sure he is interested in that. he skipped right over my comment. 
Chucke, sorry I didn't respond to your post. I was otherwise involved.
So here's the update. I've tried working on different songs to see if the issue is with that particular song, maybe something corrupt on that song. One song I tried, an older one, worked like a dream. I was in heaven cuz everything was running like a champ. Thought I had it figured out. Tried a different song, and the issues arose again. There is nothing consistent, and I can't reproduce anything.
However, I'm seeing a consistent problem with some songs when I close it out and exit Sonar. Sometimes when I hit Close, it will just stall with the blue ball. Other times, it will close fine. Other times I'll get a Fatal Error screen, and the window always says something about Amplitube. I've tried re-installing Amplitube, but get the same results.
I'm also seeing a huge amount of background processes in Task Manager. The only apps running are Sonar, but there is tons of other stuff listed under Background Processes. They're not using much CPU according to the Task Manager, but it seems like a bunch of unnecessary stuff.
Also, when I boot up, it seems to take at least 10 minutes before I can run Sonar effectively. Brand new computer.
So I'm thinking about a full re-install of everything. I'm at a complete loss here. Driving me nuts.
i totally hear where your coming from.
with that being said...you still didn't answer 2 of the 3 questions i asked
-Make sure you have all the latest updates for windows. (Sonar Platinum needs these updates to run correctly).
-check your video driver is up to date. onboard or video card. (Sonar Platinum needs this to run correctly).
Jeff, try opening your project in safe mode.
Hold down SHIFT while double clicking on the sonar icon.
then one by one load in your plug ins. see if this gives you any kind of clue as to what is going on.
Ken brought up a good point as well, is it the latest Amplitude ?
(he also mentioned what i did about the updates, wink...wink)
if i remember correctly, Amplitude uses quicktime as wll as some open GL.
so updates are freakin critical in order to run at top performance. sometimes even sub par performance.
you sound like you have a good DAW. that shouldn't be the problem unless the guy who set it up failed on a few things like :
power settings: set it to high performance. (its not a laptop)
Focusrite driver settings. be sure to run it in ASIO Mode. (make sure you have the latest drivers.)
MOBO: make sure the onboard video card is the latest version (especially if your running windows 10)