Trouble with editing fields of prefab instance

I've made CustomEditor for one of my classes and it works great except of one little detail: when I edit properties of prefab's instance, those are reverted to prefab's values at the start. But I can modify properties of other classes that don't have CustomEditor with help of inspector and they behave just as expected. What am I missing?

Here is some code for those who will ask for it:

 using UnityEngine;
 using System.Collections;
 using UnityEditor;
 
 [CustomEditor(typeof(Controller))]
 public class ControllerEditorScript : Editor
 {
     bool info = false;
     bool gameSettings = false;
 
     Controller thatController;
 
     void Awake()
     {
         thatController = (Controller)target;
         specElemSize = thatController.goal_specialElementsList.Count;
         packagesSize = thatController.goal_packagesList.Count;
     }
 
     public override void OnInspectorGUI()
     {
         thatController = (Controller)target;
 
         #region Info
         info = EditorGUILayout.Foldout(info, "Info");
         if(info)
         {
             thatController.score = EditorGUILayout.IntField("Current Score:", thatController.score);
         }
         EditorGUILayout.Space();
         #endregion
 
         #region Settings
         gameSettings = EditorGUILayout.Foldout(gameSettings, "Game Settings");
         if(gameSettings)
         {
             thatController.mode = EditorGUILayout.TextField("Current mode", thatController.mode);
             thatController.spawnCounter = EditorGUILayout.IntField("Spawning at once:", thatController.spawnCounter);
             thatController.delayTime = EditorGUILayout.FloatField("Delay between spawns:", thatController.delayTime);
             thatController.startSpawn = EditorGUILayout.IntField("Spawning at start:", thatController.startSpawn);
             thatController.AmountCap = EditorGUILayout.IntField("Max food:", thatController.AmountCap);
             thatController.maxDistance = EditorGUILayout.FloatField("Con. distance:", thatController.maxDistance);
             thatController.charge = EditorGUILayout.FloatField("Charge :", thatController.charge);
             thatController.ExplosionForce = EditorGUILayout.FloatField("Explosion Force:", thatController.ExplosionForce);
             thatController.helper = EditorGUILayout.ObjectField("Helper :", thatController.helper, typeof(GameObject), true) as GameObject;
         }
         EditorGUILayout.Space();
         #endregion
     }
 }