Stacked with excatly the same problem.

What this code does is change label above objects(in my case players) head. Inside OnInspectorGUI:

EditorGUI.BeginChangeCheck();

int currentScore = EditorGUILayout.IntField(...)

if (EditorGUI.EndChangeCheck())
{
    (sp.objectReferenceValue as Object).ChangeLabelAboveObject(currentScore);
    EditorApplication.QueuePlayerLoopUpdate();
    GUI.FocusControl(null);
}

Explanation: sp - SerializedProperty, Object - any MonoBehaviour you like.

But the main: everything goes ok when I added EditorApplication.QueuePlayerLoopUpdate Hope this will help some1, because I was looking for this for hours.

Stacked with exactly the same problem.

What this code does is change the label above objects(in my case players) head. Inside OnInspectorGUI:

EditorGUI.BeginChangeCheck();

int currentScore = EditorGUILayout.IntField(...)

if (EditorGUI.EndChangeCheck())
{
    (sp.objectReferenceValue as Object).ChangeLabelAboveObject(currentScore);
    EditorApplication.QueuePlayerLoopUpdate();
    GUI.FocusControl(null);
}

Explanation: sp - SerializedProperty, Object - any MonoBehaviour you like.

But the main: everything goes ok when I added EditorApplication.QueuePlayerLoopUpdate.

Hope this will help someone, because I was looking for this for hours.