Loren, the submissions don't appear in the count of submission for assessment until after the maxeditingtime, that's usually 30 minutes after they are submitted. They do, however, appear in the Admin page "instantly". But I'm sure you know that.
The only thing that different from my exercises is groups. I wonder if that's doing something. I'm updating my production system this week (as it's vacation here). I'll do some testing.
General plugins
Exercise module add-on: Missing Students
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