The only reference I could find to this issue was a "fixed" problem from a few years ago.
It seems to happen 90% of the time, except in rare circumstances where it magically fixes itself until I make one tiny unrelated change to the mission.
It wouldn't be an issue if it was just an error that didn't affect things, but I expect it has something to do with why a large percentage of the profiled units don't move, and when spawned in the AI stand around gormlessly doing nothing.
I'm using Vcom and custom factions, as well as a few other mods like RHS. My next test is to run without vcom, then totally stock factions, and see if it keeps happening but I thought I should post here for any ideas.