I think this CSS might take care of the problem:
/* to fix admin menu at bottom of page - http://drupal.org/node/1588158 */
body.contextual-links-region { position:static; }
It seems to be caused by CSS position set to relative for the body element. See http://drupal.org/node/1588158#comment-6180760
I had this problem myself, and notice that also, disabling the Skinr UI module - not Skinr itself - fixes the problem.