It's a Ubuntu Unity GUI bug, the standard menu location was moved to the top of the screen in all applications by Canonical. They don't intercept Qt menus consistently with their Gnome mods. Developers of apps like Firefox have made patches to compensate for Unity suckage. Apparently the menu might occasionally come back if you minimize/maximize a few times or close and restart.
https://github.com/bitcoin/bitcoin/issues/1242The server=1 command only turns on the RPC server (you also need a rpcuser/rpcpassword options in bitcoin.conf for it to work). It will still launch the Qt GUI if you are running bitcoin-qt.
You can open a console window when Bitcoin is running and access bitcoind to do your RPC work:
./bitcoind help