If you snap one of these keys on the 2d axes disappear? if yes it means that they are only displayed and then the .pdf prints them, but they are not actually traced in the drawing. turn off the display of axes. you should make annota->showsmodel to track them. I have wf 5.0 for a while and I don't remember how it was exactly in wf 4.0.
In the previous releases they activate with the display/hide command (the icon with the symbol of an electric torch).
And yet it seems that the show/erase command... used it.
but when you use the command, do you agree to the button?