Check the table travel for the z axis using stepconf wizzard. It needs to be like -60 to 15.
I tried 15 to -60 and that froze the z axis.
Edit, placed this in the wrong tread.... Too enthousiastic I found a solution.
Have you run the latency test with the suggested "abuse"? I also had strange stuff going on with the z, just as you describe. I found that my latency numbers were too low and entered higher ones. This slows your machines speed but may get rid of those symptoms.
Sven
http://www.puresven.com/?q=building-cnc-router