Whenever I use the Animal Allegiance shout (for example, on a group of Falmer and Chaurus), the affected Chaurus end up attacking or being attacked by any summoned Dremora Lords that I have. The affected animals still act the way they are supposed to towards me (by not attacking me). It doesn't seem to matter when I use the shout and when I summon or re-summon the Dremora Lords. I have not tested if there is any similar behavior with Kyne's Peace or Calm spells.
This may be related to an issue where animals affected by AA will continue to fight followers that they are fighting when the shout is used, but I can't be sure of that since the issue doesn't go away when I summon things again.