SerializedObject data getting wiped when apply to prefab?

Like so many others I am having terrific frustrations trying to get a custom editor to set data on my objects/prefabs and have it save. After following the guide on this thread, my code looks like this:

First, the storage container class and the actual custom component:

Code (csharp):

1. [System.Serializable()]
2.     public class CreatureAnimationPair : Object
3.     {
4.         public string animationHandle { get; set; }
5.         public CreaturerAnimationType type { get; set; }
6.    
7.         public CreatureAnimationPair (string animationHandle, CreatureAnimationType type)
8.         {
9.             this.animationHandle = animationHandle;
10.             this.type = type;
11.         }
12.     }
13.    
14.     [System.Serializable()]
15.     public class CreatureAnimation : MonoBehaviour
16.     {
17.         public List<CreatureAnimationPair> animationPairs;
18.        
19.         ...
20.        
21.     }

Then, the editor class:

Code (csharp):

1.  [CustomEditor(typeof(CreatureAnimation))]
2.     public class CreatureAnimationEditor : Editor
3.     {
4.         SerializedObject creatureAnimationSO;
5.         CreatureAnimation creatureAnimation;
6.    
7.     void OnEnable ()
8.     {
9.         creatureAnimationSO = new SerializedObject(target);
10.         creatureAnimation = (CreatureAnimation)target;
11.        
12.         Animation animation = creatureAnimation.gameObject.GetComponentInChildren<Animation>();
13.         if (animation != null  creatureAnimation.animationPairs.Count <= 0)
14.         {
15.             List<CreatureAnimationPair> newPairs = new List<CreatureAnimationPair>();
16.             foreach (AnimationState anim in animation)
17.             {
18.                 newPairs.Add(new CreatureAnimationPair(anim.name, CreatureAnimationType.None));
19.             }
20.        
21.         creatureAnimation.animationPairs = newPairs;
22.        
23.         EditorUtility.SetDirty(target);
24.         EditorUtility.SetDirty(creatureAnimation);
25.         creatureAnimationSO.ApplyModifiedProperties();
26.     }

In this case, CreatureAnimationPair is an enum set I've made. When I use this on a creature instantiated in the scene, it'll go through all its animations like I want it to and fill out the list of pairs. I can see them in the inspector using my custom GUI just fine. But as soon as I apply that to a prefab version of the creature, all the data in that list gets wiped -- all the strings are emptied and all the enum values become garbage. Why is this happening? How do I get the changes I make in the scene to persist into the prefab?