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It was reported by @marcopanichi in closed issue here:
Same problem occurs with Admin-Menu Plugin
The solution is to add a line to /includes/ckeditor.utils.js in order to consider the #admin-menu div:
if( drupalTopToolbar.length==0 ) drupalTopToolbar = $('#admin-menu', Drupal.overlayChild ? window.parent.document : document);
I added the line below this one:
var drupalTopToolbar = $('#toolbar', Drupal.overlayChild ? window.parent.document : document);
It's not an elegant solution, but it works for me...hope it helps!