If this happen, the reference designator >NAME could be too far away from the component, and sometimes, when you use the SHOW command, it will not show up. Most of the time these components have been smashed, to have better option to place the refdes on the right place.
In this case I "unsmash" the component, which bring back the designator back to the component. After that I smash again and adjust the refdes to the right size: 1mm, 15% thickens and vector font. For me that solves this problem.
I'm a Altium Designer user as well Eagle user, and I must say that the Eagle "smash" function is a completely nonsensical option, a mistake the Eagle developers have make a long time ago and never did solve.
I am even more surprised that Eagle does not understand electrical connections in schematic as well in pcb layout. I often need to move components in schematic because they have only visual connection but not electrical.
Also you can have wire over each other with same and different netnames!
In PCB layout you have to route a track with a precision of better than 1um to the center of a pad before Eagle understand that it has been connected to that pad.
Eagle is a very buggy program, in Altium Designer you could design your pcb two or three times faster! But some customers seems to be married with Eagle...