Custom Fields area showing instead of drop downs, updates will not persist.

Since upgrading to WP 3.8 and AegaeusWP 4.0 I can no longer add side bars to post. The Custom fields area which used to have drop downs, now contains fields, and those fields, will not update even if the correct data is put in them. Please see the Screenshot linked.

Please help with this strait away. I have already re-installed the theme which had no affect.