That's an interesting suggestion. It didn't cross my mind that it might have something to do with the amount of stealth units. It may still be one of the new events causing some problem or another, there are lots of new events and their complexity makes it easy to miss something small, but I'll investigate all angles. If it does have something to do with stealth units, it's possible SBON3 (on hard mode, at least) or, more likely, S17V1 might also give you trouble. If that's the case, it could narrow down the problem even further.
I'm relieved to hear it works like a charm otherwise, and only those maps so far have presented a problem!
Thanks so much for the update. I'll keep looking into those missions when I get the chance, and hopefully can figure out what it is fairly soon.