Hi Ken,
I'll keep an eye on the settings, but am pretty sure it was enabled and the darks where checked with the pause symbol waiting for their turn. For both my memory is foggy as I find these things out first thing out of bed. The first sequence, I cannot recall clear enough if iniated the darks after waking up or if the recovery dialog was still open and waiting. The second sequence, though, was in its finished state. And I remember specifically looking at the setting in both the sequence window and global prefs, and it was checked. Same with darks.
I'll keep a detailed log of what happens after a session if this happens again and will report back here.