Yep. A very simple mod will fix it, too. I expect that the commander just needs some undead leadership - not necessarily enough for the whole mob.
For example, some random events give forces led by a commander who doesn't have enough leadership to control the units who nonetheless start out under his command and work fine unless they get un-assigned to his command. Which is actually an interesting and not inappropriate limitation - they are under him do to an unusual event, and not only because of his innate leadership. And, he can't have an army of unrelated troops put under his command.