I have encountered a Sonar X3 freeze or hang condition that is reproducible and it's related to MIDI routing, I think.
I submitted the data, project file and (Task-Manager-forced) crash dump as CWBRN-20028.
 
I wonder if this happens to others with a similar setup?
 
Here is the setup:
I route an instance of Reaktor's MIDI output to an instance of Rapture (it doesn't matter what VSTi is used).
I load Spiral.ens into Reaktor. Spiral is a MIDI automaton that generates MIDI data based on spiral patterns.
That MIDI data is sent to Rapture's MIDI in.
 
I repeat this two more times with two more Reaktor tracks and two more Rapture tracks (or any VSTi).
 
When I run this setup, sometimes not all tracks will be audible, but that's not the problem.

If I try any sort of manipulation, like muting or soloing tracks, sooner or later Sonar X3a (211) will freeze, usually immediately.
I can't kill it with Task Manager, I need to reboot.
I've tried all sorts of variations on this theme and I can only conclude that it has something to do with internal MIDI routing.
 
Here is the layout I use. Only simple instrument tracks, Prochannel is OFF on all tracks.

http://www.arachnaut.net/audio/Sonar/CWBRN-20028/Sonar-Layout.png
 

 
Here is what Spiral looks like:

http://www.arachnaut.net/audio/Sonar/CWBRN-20028/Reaktor-Spiral+Rapture.png
 

As a point of reference - this works in Live 8.4.1 (64-bit):
 

I captured this using Camstudio (no audio) and coverted to Flash Video. This time it crashed, rather than hang. I sent this crash dump to Cakewalk with the trouble report.
 
http://www.arachnaut.net/..o/Sonar/Sonar-Crash.flv

You mentioned sometimes not all tracks being audible. If Sonar is dropping MIDI notes, that could be due to the MIDI buffer size being too low. Have you tried increasing it to 500 or more? Also, what's your audio driver buffer set to?

The MIDI buffer is set to default (250 ms). The MIDI data rate from Reaktor is not much different from what a person would generate - a few notes per second.
 
Audio driver is 256 samples ASIO.
 
I don't think this is it.
 
Noel's blog entry mentions this:
 
http://blog.cakewalk.com/developer-notes-sonar-x3-vst-enhancements/
 
I quote near the end:
 
"Additionally a longstanding problem with multiple MIDI out VST plugins causing a SONAR to hang was addressed."
 
 

I can make an absurdly ridiculous number of these tracks work fine in Live:
 
http://www.arachnaut.net/audio/Sonar/CWBRN-20028/It-Works-in-Live-8.4.1-quite-well.png
 

[Off Topic]
I'm fairly happy with my computer setup's performance. Here is an example of an extreme from another forum where people were saying that NI Monark was a CPU hog (I was bragging a bit):
 
http://www.native-instruments.com/forum/showthread.php?191811-reality-check-monark-versus&p=1163065&viewfull=1#post1163065

At one time there were long-standing issues with routing midi from VSTis back into Sonar's input. Similar problems were discussed.   Perhaps that is the problem Noel's blog referred to. Not to say this is the same as your problem, but definitely send in all your findings by the problem reporter. They may not have caught every bug.

arachnaut
The MIDI buffer is set to default (250 ms).

Increasing your buffer won't help with the hang, but it may help with tracks going silent or dropping some notes. The old default was 500, and 250 has proven to be too small for many systems - without any particular correlation to the horsepower available.

Sonar does not differentiate midi channels with multiple soft synthe sending midi out. This is one of my big peeves.
http://m.youtube.com/watch?v=73Pf1b6bTk8