I can reproduce. The problem is that LyX does not know the refresh the
menus for some reason. So when you start a new document, the menu
options available are as if you had no document open. I'm not sure why
this is happening.

I have found a (partial) workaround: if you press "alt" in Ubuntu it
brings up the HUD which searches the menu of the open application. For
example, if I press alt and then "sett" it shows me "Settings
(Document)", meaning that it found an entry under Document that matches
my search string. I can then press return and it is as if I went to
Document > Settings. In LyX, after I open the HUD and type a letter, all
of the menus are refreshed. However, you have to do this each time you
want the menus to be refreshed.

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https://bugs.launchpad.net/bugs/1430059

Title:
  Many options in various menus appear greyed out, inaccessible

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