Finally, after hours and hours of trying to figure this out I now know how to replicate it. Using the setlist in either X3 or Platinum with projects that have Kontakt running causes a major crash. Between sets I froze the Kontakt modules in the synth rack and everything played fine.
I didn't see this posted anywhere before, so here it is. I'm not sure which is to blame - Cakewalk or Native Instruments, but the problem didn't happen until Platinum was installed.