If you re-position the editor windows and hit save layout, the layout is not saved.
1) reposition the main editor window and blueprint editor window
2) hit the save layout button
3) restart the editor and the window positions are lost.
I tried this with killing the editor in visual studio and shutting down the editor gracefully and got the same results.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-13533 in the post.