I was having the same issue that the original poster asked about and I believe it is related to the Dynamics UCS setting/system variable.
Hovering over the icon in question, I get a pop-up display with two lines the first line listing "Snap UCS to active solids plane - On" and the second line listing "Dynamics UCS - UCSDETECT (F6)". After changing the setting to "Off" I no longer see the line "The object is an external reference" appear in the command line.
If you use the function keys on your keyboard to turn settings on and off like I do, you may have just accidentally hit F6 and turned this setting on. Hope this solves your problem.