Still trying to figure out what circumstances were the same that differed in other times, but it appears fairly random at the moment. One thing I have noted is that once I used Alt-Tab to try to swap back to another application and it had immediately highlighted the 3rd one along, not the second as expected. This seemed to indicate that possibly the second application (explorer in this case) had focus instead of pontifex. I haven't seen it since to verify one way or the other :/