The scenario is as follows. In a hypothetical future drive I spend energy E to accelerate a mass of propellant m to velocity v (e.g., plasma state propellant in the very powerful circular accelerator), so $v = \sqrt {2E/m} $.
Then I use my accelerated propellant as exhaust for my jet engine, using all mass in time t, getting thrust:
$$T = vm/t $$
Then my spaceship of mass M will be accelerated to speed (assuming m<<M):
$$V_1 = Tt/M = vm/M = \sqrt {2E/m}*m/M = \sqrt {2Em/M^2} $$
Now, if I spend the same energy E directly to accelerate my ship (by some unknown mechanism but transforming all energy E into kinetic energy of the ship), I get: $ E = MV^2 / 2 $ and $V_2 = \sqrt {2E/M} $
So, $V_2/V_1 = \sqrt{M/m}$ and my ship's velocity in the 2nd case is much bigger than in the first, while I seem to have spent the same amount of Energy in both excercises.
I am sure I am missing something very obvious but for the life of me can't figure it out, my physics became a bit rusty I guess :( Any pointers appreciated - why this difference? where does the energy "disappear" in the 1st case?