I've been using the exact same project template for about a year. It basically consists of the following:

-16 MIDI tracks routed to one instance of Engine (Best Service's sample player)
-16 MIDI tracks routed to Kontakt
-16 Audio tracks, each with two instances of Slate VMR; the first has VCC preloaded into it, the second is empty
-16 buses each routed to a pre-master bus; these each have VMR preloaded with VCC, and about 6 of them have VTM

As I said, I've been using this exact template for a long time and it's never given me any issues, even after loading several GB worth of sample libraries and filling all of the VMRs with modules. However, starting with the last two updates, I've noticed that SPlat is severely lagging, even upon initially loading this template (before I've even started recording or processing anything). This is immediately noticeable when scrolling through the tracks. Whereas it used to look smooth as butter, now it looks like I'm watching a movie with a really poor frame rate. The tracks kind of jump in position rather than smoothly scrolling. Also, if I double-click on the console button to make it full screen, the graphics kind of fill in from left to right rather than immediately changing to full screen like it used to.

I haven't changed anything in my template between SPlat updates, yet my system is running this template more and more poorly.

I tested whether a simple project runs poorly or not by loading a blank project and just filling it with MIDI and Audio tracks and it runs perfectly smooth.

So, I know that the plugins I have loaded are for some reason not playing nicely with SPlat anymore, but I want to know the reason. Again, this exact template, even when fully loaded with VIs, modules, and tracks used to run without skipping a beat. Now it's stuttering graphically from the start. Also, as the project gets more complex, I'm getting CPU spikes and audio glitches.

Lastly, simply saving my project takes at least 10x longer than it used to. Before when I'd hit CTRL+S, the project would save in about 1/2 to 1 second. Now it's taking upwards of 10 seconds to save. This is even when there's nothing loaded except the initial template. What in the world is going on here?

This is very frustrating. Any tips on figuring out the source of all this trouble would be greatly appreciated.

Thanks everyone!

Have you tried to rollback Sonar and see how it works in older versions now?

Certainly there were also updates from windows.
Take a look at the energy options. Maybe the harddrive sleeps after 5 minutes and thats way saving takes a long time.

I have had similar glitches/problems with Sonar X3 producer recently. After much investigation, and prompted by a post on this forum I read from some years ago,  I potentially traced the problem to  a tempo change in my project that I had no idea was there. The tempo map showed a change from 85 to 500 at measure 18 - but the project did not speed up at this point. I effectively lost my project - it was so slow to respond every change took upwards of 30 seconds,and my graphics were like a stuttering stop motion film. In another project key meter changes were introduced but I'm not sure if this was due to me in the pasting of clips process where the dialogue asks if you want to copy tempo and/or key meter changes. It's just a suggestion - check on the tempo and key meter maps/lists to see if some unintended changes have taken place.

some times i have had a song which shows this issue and have found that if i create a new one although identical as the first the issue is not there. it didn't happen often only once or twice but starting it from new solved it. yes it can be a pain depending but for me it has worked even though everything was the same like plugins number of tracks and everything.

Process of elminiation.
First I would troubleshoot this by bypass all fx plugins, shortcut e.
If the problem still persists unload your virtual instruments one after the other.
 
Check your cpu utilization with windows taskmanager. Maybe a task in the background consumes many cpu cycles and critical slow down your system.
 
One sidenote regardless of your current problem. It's better to use 16 instances of a vi instead of 16 midi tracks to 1 instance. This is because Sonar can distribute only complete instances of an instrument to the cpu cores. If you have one instance of Engine, then this one will be running only on one cpu core.
 
-Markus