I don't know how to reliably reproduce this yet. What happens is as follows:

1. Loaded a job into scheduler and turned scheduler on. This job has a sequence which will run 300s exposures
2. In capture, go after an entirely different target with an ad-hoc sequence set to 60s exposures NOTE: The job wasn't scheduled to run for an hour
3. I let the thing go and come back later, I realize I have very few images

So now I check the analyze module and I see it started with 60s captures, took about 4/10 and then continued on to take more, but swiched to 300s.
The really strange thing is that while it acted like it was doing 300s exposures, I don't believe that they were - the images look too tight (no guiding!) for 300s captures, and I would have expected most stars to saturate.

I think I had the logs for the CCD and Align turned on, unfortunately not for capture. I'm going to turn on logging in case it occurs again.