While researching this issue I noticed some commonalities between the sites affected.
1.) While inspecting the assets being loaded by each I noticed a javascript file named admin-bar-rest.js. This file comes from the notifications portion of the JetPack plugin. It seems to be inserting itself into the admin bar in order to enable notifications from wp.com. Right now I believe this may be the main culprit.
2.) All sites affected by the issue are running the Atahualpa theme.
3.) All sites affected by the issue are running JetPack.
4.) All sites are (I think) domain mapped to gc.cuny.edu. (no commons subdomain)
There are six sites that fall into the above conditions with one difference:
These two are not domain mapped and therefore are not experiencing the issue:
Gslis720 Digital
Keith K Miyake at the CUNY Academic Commons
These sites are domain mapped and therefore are experiencing the issue:
Committee on Globalization and Social Change
The Center for Place, Culture and Politics
The Committee for Interdisciplinary Science Studies
The Committee for the Study of Religion
So I think what we're seeing here is a conflict between Atahualpa, JetPack and domain mapping. I'm not sure yet exactly where the conflict is occurring but I wanted to update here incase one of you sees the problem before I can.
Boone, you mentioned that there have been some customizations to Atahualpa, could they be introducing this issue?
I've added Ray as a watcher here because he's a watcher on the duplicated issue #1508.
