robert_e_bone
I did some poking around - here is a thread that has a reported issue on crashes on a 2nd instance of Microtonic:
 
http://forum.cakewalk.com/Sonar-producer-x2crashes-when-opening-projectswhen-closing-projectsmany-other-problems-m2824295.aspx
 
Does your computer sleep?  That was discussed in the above thread.

I remember that thread. Funny how I forgot I posted that. Well, it seems like my problem still continues! I still sleep my computer on a nightly basis, but if I plan on working on some music, then I do a full restart before opening Sonar for that session. That's my new policy, and so far, it has help with other issues. And for all of the tests that I have done in my long-winded first post, I made sure the computer was restarted each time.

Brando, have you had a chance to test?

2:43AM
Brando, have you had a chance to test?

Hey Tony - 
Sorry - I completely forgot about this post. I finally picked up your PM today and figured I would give this a try. I am also using the 64 bit version of Microtonic, also version 3.1.0. SONAR X2a (64 bit) in Windows 8.
I started out with just a single instance of Microtonic, synced to a project with Jamstix (16 tracks) and one instance of Lounge Lizard with an instance of Strum Electric. There were a couple of effects on both of the synths (Overloud VKFX etc) and Input Echo was 'on' on both of the AAS synths. I also had an instance of Permut8 in the Fx bin of the instance of Microtonic receiving MIDI from a MIDI track.
Everything was good, Microtonic synced right up with Jamstix, no glitches, no gaps, etc.
I added a second instance of Microtonic, selected a different preset, and repeated - same thing.
I added another instance - and then another. In a nutshell, I was able to load up 6 instances of Microtonic and had no problem - no glitches, no crackles. The CPU climbed only slightly with each instance. I didn't stretch it to the breaking point since you said you had a crash with two instances of Microtonic. 
(In fact - while I was drafting this I went back to my DAW and tried another couple of instances - I did get X2 to crash while I was playing around with a 7th instance of Microtonic.)
The cpu didn't get objectionably high - so I don't know if this is symptomatic of a problem with Microtonic or with SONAR. 
If there is something else you want me to try out - let me know -  
 
 
 
 

After sending 2:43AM a PM to point him to this thread, I just tried a project with 4 instances of nothing but Microtonic - and got a crash after about two minutes. (SONAR crashed to the desktop and otherwise exited gracefully).
I'll repeat the exercise with just two instances, and then with one later today - just to see. 
Maybe it's a clock/transport issue? - Previous project had Jamstix 

Curiouser and curiouser - 
I started a project with nothing but Microtonic. First a single instance - and let it play away at 120 BPM - I stopped the transport at 5 minutes.
I added a second instance of Microtonic - so nothing in the project but 2 instances of Microtonic.
I can play either instance from its own GUI Play button independently, but when I clicked the main transport Play button, I got an instant crash and SONAR poofed out of existence.
I am going to try to repeat the situation with Jamstix and Microtonic - 
Hmmm.....

Based on the above, I initially tried a project with just Jamstix (16 tracks as previous) and 2 instances of Microtonic, and was happy to see that the project played perfectly, as it did last night. I could stop and start the transport, rewind, etc and each time the project played normally. Even more interesting was the fact that the Jamstix "song" is roughly 2:55 seconds long, but I could keep the transport playing longer, so that even with only the 2 Microtonic instances playing, everything seemed solid.
 
On repeating the exercise, however - a new project instance of the same configuration (Jamstix plus 2X Microtonic) - the project played for 55 seconds then crashed. 
I am a MIDI ignoramus and don't know enough about timing sync when using soft synths - it appears that Microtonic has difficulty when behaving as the master - or maybe the two instances have difficulty in figuring out who should lead. I initially thought that Jamstix fixed the problem, but now it appears that while it alleviates it, it still exists.
I hate crashes so I am going to leave this and try to get something done - 2:43AM - if you have some thoughts and want some follow-up on helping to track down the nature of the issue - let me know.
 

Brando, you are the man!  There is something VERY STRANGE going on here!  Thank you very much for testing and posting your results.  This is a weird issue, indeed.  Early on, I pointed the developer of Microtonic to this thread. I hope he is reading it and staying up on the results. If so, I bet he's as puzzled as we are!
 
Well, I just tried a new, blank project and added one instance of Tremor.  I then proceeded to add three Microtonics before Sonar crashed and Windows asked to close the program.
 
Up to 2, it seemed stable.  I will try again and see how long it goes.
 
Brando, when you're adding each instance of Microtonic, are you putting the Microtonics into the same FX bin of one audio track, or creating a new audio track and then adding each new instance to its FX bin? I am doing the latter.  Just want to confirm your process.
 
I know you have things to do, and crashes do indeed suck, but if you don't mind...please take a peek at the Windows Event Viewer to see what appears in the Application Log at time of crash.  I get repeated Sonarpdr.exe and ntdll.dll faults.

Neither actually. Microtonic is set up as a synth here. I just do an "insert soft synth" and select Microtonic from the pull down menu for each instance. I won't have a chance to look at it again tonight but will try to take a look tomorrow.

Incidentally I almost exclusively use simple instrument tracks for my soft synths here despite some concerns about them on these forums. So that's what I used here but with input echo disabled on each instance.

2:43AM - 
I initiated another crash this morning, and checked the Windows Event Viewer for this and the previous crashes from yesterday - 
All are Application Errors (1000), showing SONARPDR.exe as the faulting application,
The faulting module is MSVCR110.dll ( x 5), 
KERNELBASE.dll (x 1), mfc110u.dll (x 1), and ntdll.dll (x 1)