You got it!
When you mentioned about “recognizing the logged in user” it reminded me about the authentication plugins I am using. “HTTP Authentication” and “Members Only”. (They allow me to authenticate people through http). I had one botched up option in “Members Only” and that was doing it.
Of course when I disabled the plugins to make sure they weren’t causing the issue I wasn’t able to see the admin bar. Because with those plugins disabled there was in fact no logged in user.
Thanks a lot for your help!