The cockpitweb software misses a few tests out that CTC use, such as the colour shape grid, shape within shapes task and as stated the final deviation/shapes/number test.
Also i find the flying through squares on cockpitweb really isn't very good, also when doing pilapt I found the joystick was a lot more sensitive than I first expected it to be and ended up flying everywhere at first.
However the software as far as I know is still the best practice tool you can get for the aptitude test.