OK I think I figured it out. I downloaded by sub exposures and I looked at the exposure times for my "blank" frames. They were 1/10 of a second... the good ones were 60 seconds, as expected. I could clearly hear the shutter opening and closing on my bad frames, and it was just as long a duration as the good ones. Clearly some sort of software thing going on here.

I searched the forums and came across this topic this topic and they symptoms sounded pretty similar to mine. After some persistent fiddling around and a little luck I'm pretty confident that I figured out the problem.

I need to set "Force Bulb" to "OFF", and "Mirror Lock" to "0".

I was able to reproduce the problem, and I also learned that once the system exhibits that failure mode, I need to restart everything to get it working again.

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