What if your time spent traveling in zero space is not actually spent at the "zero space" point, but merely traveling through the area of the "cone" to the "zero" point, and then back to real space? My guess would be that the Andalites don't actually reach the zero point doing it this way either- they just get close, but still have to travel some real distance too- that explains not only why it takes time to travel through z-space, but why it seems to take longer in z-space to travel a greater real space distance. Honestly, calling what Andalite ships travel through "zero space" is a bit presumptuous if you look at it this way (I'd go with "condensed space" or "condensed sweetened space" =P).
Then, of course, the shifting of z-space is pretty easy to explain. Visualizing it as a perfect cone is a bit flawed. It would have to be a cone that's constantly rippling and twisting with the changing energies of the universe. If a ripple happens to fall along the condensed space line of travel between you and your destination, it could severely alter the travel times between those two locations. Space, even n-dimensional space, is far from "smooth."
