It is indeed very peculiar if it works in the GUI now but not on the command line, there is no particular reason for this as I can think of (as the gui essentially calls the command line functions). I seem be running the same ubuntu as you but there could of course be many other differences with packages installed or not.
fenics-dijitso (2019.2.0.dev0)
fenics-dolfin (2019.2.0.dev0)
fenics-ffc (2019.2.0.dev0)
fenics-fiat (2019.2.0.dev0)
fenics-ufl (2019.2.0.dev0)
distro-info (0.18ubuntu0.18.04.1)
Please note that, I have released a FEATool update 1.13, although it shouldn't change anything with respect to FEniCS really, you might try and see if it helps anything (I think it should fix finding fenics in the sysinfo, but maybe not much else).