Yes, we made some improvements in late 2014 to make the Content Outline more responsive, particularly for people who have large, flat folders, using a system of proxies.  It works quite well, except when it gets tangled up.  Things can get get misplaced.

It appears that you can cause the proxies to flushed and rebuilt from scratch by commanding an Undo or Redo operation.  For example, delete a bookmark (I would recommend one which is not misplaced), and then click in the menu: Edit > Undo.  The deleted bookmark should come back and all bookmarks should move into their proper places.

I would be interested to know whether or not that works.  Also, because these misplacements occur only very rarely for me, if you vaguely know how to reproduce it, I'd appreciate that information.  Even better would be if you could send us the .bkmslf document which exhibits the issue.  Sending it via our Trouble Zipper
Jin