My Sonar is breaking down.....

1) ASIO or WDM? Edit - Sorry you answered this - it is ASIO - have you tried WDM?
2) USB 2.0 or 1.1 (the port on your PC you are plugged in to) (or 3)? Also are you plugged directly in or into a hub (if Hub, is it powered or unpowered)?
3) What bit rate and frequency of your recorded tracks?
4) Other USB devices - 

Windows does all sorts of things even when you think you're not using it that much.
Registries get affected for the most when you:

- install/uninstall programs
- install/uninstall hardware
- run updates
- move folders locations (especially important for VST libraris)
- run supposed "pc tune up" applications
- setup windows to self optimise (or destroy )
 
If you say that you didn't used to have this problem but now you do, maybe something happened there.  The reason why I go down this route is because of your mentioned blue screen.   If it was a Sonar/Audio/Latency issue, at worst Sonar would have crashed.  But a blue screen???  That screams drivers/registry to me.
 
Do you get the crackling sounds now on other projects too or only the song you did the other night?

Hi Jon,

Due to the BSOD, I'd test your system's RAM and stress-test the system as a whole.
If you've got a bad stick of RAM... or a hardware issue, Sonar X1 (or any other DAW app) is going to have problems.

As was suggested, check your DPC latency.  If there are large spikes, that's guaranteed to cause glitches/dropouts.
If your idle DPC latency isn't low/consistent, you'll have to run the Emu at larger ASIO buffer sizes.
If there are spikes well into the yellow/red, those will need to be addressed before you can effectively work.

Also, check to make sure all HDs are running in DMA mode.  If one slipped into PIO mode, that'll absolutely kill performance.

Another thing to check:  Make sure the Emu is connected to a USB 2.0 controller (not a 3.0 controller).
Most USB 3.0 controllers are provided via 3rd-party add-on controllers (not integrated into the motherboard's chipset).  Using these controllers can result in poor performance... (similar to using a "rogue" chipset Firewire controller with a Firewire audio interface)

You might open Task Manager in Windows, go to Performance Tab, start the project, and watch your CPU and memory usuage.

I had this problem on a project that was using Hollywood Strings.  CPU usuage would go up to 100% and the noise began.  Solo isn't a true test because it turns off a lot of processing demand.

I had to solve this by (1) making a copy of the project under a different name, (2) deleting everything but Hollywood, (3) bouncing to audio, and (4) pasting the audio back into the original project.  I saved the original project with the audio under yet another name, and deleted the original Hollywood tracks, keeping only the imported audio.  Never lose your original source tracks!   I'm sure you know that. 

This could happen with any virtual instrument or set of instruments.  In my case, my PC was always able to handle things until this project in which Hollywood took it over the top.

If you don't have a ton of tracks or any high-demand VIs, then this isn't it.
 
Is that you and your band in the picture?  You had a lot of soft synths on Penny Lane.