Probably being a noob idiot but...

[Redeyes]

Did you attempt to exit the game and starting it again?

I had this problem when playing at certain resolutions. Playing it in windowed-mode mostly solved it for me. The commanders tended to disappear for me after having been in the army setup menu.

There's an unrelated problem where the whole UI disappears, but it's related to the copy protection.

[Colonial]

It is true that when I closed and re-opened the game the problem was gone. but as I've said I was playing a different save game by that point...

[Radio_Star]

Originally Posted by Redeyes

The commanders tended to disappear for me after having been in the army setup menu.

This happens to me pretty often while playing the first turn after loading a saved game. Closing dom3 and restarting fixes the problem.

[Colonial]

brillient.

If it ever happens again I will try that.