PositionHandle causing me problems

I am trying to right a very simple editor script to show some waypoints for my charcater to move around, I have it working and the editor script shows the points. But for some reason if I use Handle.PositionHandle I cant select the handles or get them to move but if I change the line for Handle.FreeMoveHandle then everything works just fine. I think it is somehow connected to the GUI.SetNextControlName but I just cant get it to work, if anyone can let me know what I am missing that stops PositionHandles from working when FreeMoveHandles work just fine I would be very grateful. Below is the OnSceneGUI() method I have in my editor script. I am using control names so I dont have all the waypoints showing PositionHandles as that gets a bit much when lots of points have been placed.
If I change a value in the inspector or click the 2d icon to switch between 2d and 3d makes the position handles work correctly, and also when the position handles cant be selected I can drag the scene or select the game view tab, it is all very frustrating.

Code (csharp):

1.    int selected = 0;
2.    string lastfocus = "";
3.  
4.     public void OnSceneGUI()
5.     {
6.         MyClass obj = (MyClass)target;
7.         Handles.matrix = obj.transform.localToWorldMatrix;
8.         Handles.color = Color.black;
9.  
10.         string hn = GUI.GetNameOfFocusedControl();
11.  
12.         if ( hn != lastfocus )
13.         {
14.             if ( hn.Length > 0 )
15.             {
16.                 if ( hn[0] == 'k' )
17.                 {
18.                     GUI.FocusControl("");
19.                     string hn1 = hn.Replace('k', ' ');
20.                     selected = int.Parse(hn1);
21.                 }
22.             }
23.  
24.             lastfocus = hn;
25.         }
26.  
27.         for ( int p = 0; p < obj.points.Count; p++ )
28.         {
29.             pm = obj.points[p].p;
30.  
31.             GUI.SetNextControlName("k" + p.ToString());
32.             if ( p == selected )
33.             {
34.                 Vector3 newp = Handles.PositionHandle(pm, Quaternion.identity);
35.                 //Vector3 newp = Handles.FreeMoveHandle(pm, Quaternion.identity, 0.1f, Vector3.zero, Handles.CircleCap);
36.  
37.                 Vector3 dl = newp - pm;
38.  
39.                 obj.points[p].p += dl;
40.             }
41.             else
42.                 Handles.FreeMoveHandle(pm, Quaternion.identity, 0.01f, Vector3.zero, Handles.CircleCap);
43.         }
44.  
45.         Handles.matrix = Matrix4x4.identity;
46.     }