By adding the conductive tube eddy currents will indeed be induced by the moving magnet which will slow it down. We know that the first system cannot be a free energy machine, and the machine you are proposing will be continuously extracting energy from the system and turning it into heat in the copper tube (the same mechanism that heats an electric toaster,current in a conductor), so it should produce even less energy. There isa certain potential energy associated with the separation of two magnets and with their positions in a gravity field, and that is the most energy you can ever extract from the system if you let it run by itself without interference.

It is simple to simply claim conservation of energy to show why this machine won't work (and it's correct) but it's also interesting to look at it kinematically. A field from a magnet typically decays versus distance(d) with a 1/d³ rate while the force of gravity is basically constant(near the surface of earth). To lift a steel ball or magnet up the ramp the force from this field at a distance must be greater than the mass of the ball times the acceleration of gravity times the sine of the angle of the ramp with respect to horizontal (i.e. Fmagnetic > m*g*sin(theta)).

With a long ramp of high slope (theta) the magnetic field will be so strong at the top of the ramp that the ball/magnet will stick to the magnet rather than falling through the hole because the magnetic force increases as it goes up the ramp. If the ramp was sufficiently short and of shallow enough slope then the ball/magnet could fall through the hole(because the force of gravity does not have the sin(theta) term for a vertical descent through the hole), but the magnet would slow it's descent down the hole, so it would not gain enough kinetic energy from the fall to be able to roll up the ramp back to it's initial starting point, and so it could not run perpetually.

I'm not sure about the setup (I'm having a hard time picturing it), but keep in mind that you're also going to be losing energy due to friction. Also, remember that an object responding to magnetic force exerts a counteractive electromotive force on the electrical current that is generating the magnetic field in the first place. If you use your static magnetic ball to do work using its magnetic field, then you will eventually de-magnetize the ball.