> Could this be a conflict with long exposures?

I've done lots of 1/2 second exposures with 3s interval, and it shoots some at much shorter interval than 3 and some 3+??? At one point, the docs said 5s was a barrier. Maybe it was the 5dmkii specifically. All of my cards are rated higher than the 5D can write (but makes DIT much faster) so I doubt it is write speed interfering. What makes me think it is not the camera is that using a cheap external timer works without skipping a beat.

Yeah, the external timer behaviour is fairly strong evidence. Curious though. These cams all seem to have a milli- and micro-second hw clock, and can both schedule and sleep against either. But it's also true that every cam has some weird quirks. And I don't know the 5d2 internals well.

From what I've seen, the image capture process is state machine based and tries to avoid sleeps and delays. Which makes sense for RTOS and professional photography.

If you care enough to debug it, pop into the discord and I can make you some tests to run.