Undo seems to be broken when moving a panel with a sprite that uses UIStretch. When you move the panel and release the mouse button you get this in the console:
<pre>
Stored Snapshot does not match same set of objects that are in the active set of snapshotted objects
UnityEditor.Undo:RegisterSnapshot()
UnityEditorInternal.Slider1D:Do(Int32, Vector3, Vector3, Single, DrawCapFunction, Single)
UnityEditor.DockArea:OnGUI()
</pre>
See screencast:
http://www.screencast.com/t/GsOqgIN4hThe plan is to have a settings dialog that slides down over the main dialog, both are stretched full screen. UIStretch doesn't work well with a 3D GUI, so I switched to a 2D GUI.