The most annoying thing with the reference manager is how it will refresh after you save a scene, often forcing you to resave it again two seconds later.
I had to deactivate the auto update.
What kind of information did you get about this feature anyway? I don't save game objects through ES3, I only use it to manage player prefs and saving and loading of variables, and I've always been puzzled by this section of the tool.
My ES3GlobalReferences file is very small. Was yours huge? Did it save a whole chunk of a scene in some way, somewhere, on behalf of ES3?