Well - if you go back to Lawp's question of 2 weeks ago, it turns out I think he had the answer.
It turns out, at least in my installation, Microtonic is set up by default to send MIDI out.
I turned off MIDI out in each instance of Microtonic, and have been running 5 instances of Microtonic for the past 8+ minutes without a hiccup. Microtonic is the only thing in this project, which would have definitely resulted in a crash previously.
(To turn it off, go to MIDI Config from the Main Menu in Microtonic, then deselect "Pattern Engine Sends MIDI Notes")
I only ever use Microtonic for its own on-board sounds, so doubt that the need to use it to trigger something else would ever be something I would use. I guess if you needed this, you would need to limit yourself to a single instance.
I know that in the past SONAR users have been critical of MIDI crosstalk errors - not sure this is a remnant of some of those issues, or a quirk in Microtonic.
2:43AM - please give this a try and let me know how/whether it works for you.