I think I see what happened. After looking at the security footage... I see it never did the Meridian Flip.
I have the Guiding Deviation set at 5. I do that because if the guiding is terrible, I don't want it taking any pictures (I assume that's what it's there for).
However, I notice that once guiding does break the limit, it takes a picture, but halts when it sees the guiding past 5. It then immediately takes another, it really needs to wait until the guiding improves.
It might have been doing this through the flip period. I did notice no images where taken after midnight.
or (what really might have been the problem)
I remember glancing at the Meridian Flip timer thinking, hey that says 4+ hours, that seems a lot... oh well, it's less than the parking time, so I didn't question it.