Note: Looking through the Gradebook History a little more, it seems like this might be affecting the same students for whom Canvas had earlier (incorrectly) set a 0 on assignments before the term, which we had to manually override.
See my ticket on this here. (It's marked as solved, but the solution that I was given seems either to be: a) don't copy courses between terms, or b) unset the 0's manually. We've been doing B, since A is not workable for us. But it seems like that may be causing other problems.)
So, in that case, are the students not getting the 0 set for a "missing" assignment, because Canvas doesn't treat it as "missing" if it had already been assigned a grade earlier? In that case, Canvas' own incorrect grade is what is initially throwing these off.