Skeinforge doesn't separate z moves from x and y moves. So with acceleration in the reprap firmware on, the feed rate ends up being too fast for the z axis since it starts with the speed from the previous move. The reprap host issues a G1 Fxx.x command before z moves to set the initial speed below the max rate of the z axis. Perhaps the new RAMPS firmware does a better job at working with Skeinforge.