Steve,
G2 (the motion control system that underlies fabmo) uses "S-Shaped Ramping" when changing speeds. This means that on a 3D terrain carving, the when the Z Axis reverses from plunging to lifting up, the speed change (-0.7ips to 0.7ips) is governed by this "ramping" strategy. Typically I keep my Z axis ramping set to 25 inches/s^3 -- that is inches per second per second per second (the rate of change of acceleration) -- this is a safe value and keeps me from pushing the Z motor too hard when it is trying to slow down or speed up to high speeds.
However, in your situation, your Z axis is never going to get to high speeds because it is constantly reversing between up and down motions. In this situation, you could afford to use higher jerk (ramping) values for Z. These settings are found in the configuration menu under "axes" -- try setting the jerk values for X, Y and Z to 4x their current value (yours will be in metric so the numbers will be different from what I referenced above).
Also, you'll want to put cap on your feedrate -- the tool won't be trying to move that fast in the 3D carving, but when it jogs into place for the cut, it can get up to high speeds. Limit that by setting your feedrate and jog maximums to 2000mm/min for X and Y and 1000mm/min for Z.
That should keep the tool under control and allow you to fly through the 3D moves a lot faster.
Brian