Why do my berserk commanders disappear after winning fights

[Bananadine]

A few times now in the same game, I've had a very powerful commander go berserk and win a battle while the rest of his side routed. Two of those times, the commander disappeared after the battle, and thereafter it was as if he had been killed.

This happened, just now, for the second time. The enemy all routed or died, leaving only my commander on the field--but now on the map, some of those routed enemies are apparently still in the province they invaded and then routed from. They are besieging my fortress, and my great commander is no longer on the map. It seems as if my .trn file is broken--as if the battle replay it shows me isn't what "really" happened. What kind of awful bug is this? How can it be avoided?