Have you checked for backlash & any free play in your ballscrew/leadscrew through the full range of the z axis? Is your machine earthed properly because Gary is one of the board experts so if he says it may be static then that is something worth checking.
I would also check the spindle is trammed correctly, that is something that you want to do anyway as part of your machine maintenance program
After I had repaired/rebuilt my CNC I skimped on the motion control which I really shouldn't have done, I ran mach3 on a windows XP machine & the cnc was conected to the computer via parallel port, having read lots of posts on the mach support forum about people having problems I made sure the computer was stripped down & the only program installed was mach3, I optimised the computer by using settings from Black Viper who I had read about on this forum.
Now my set up is completely different, I am running UCCNC & mach3 on a windows 7 computer, the CNC is connected to the computer by an Ethernet motion control board & I have had to do very little to the computer
Auto updates & power saving features are turned off but that is about all, have the vectric software installed on the computer along with a couple of other programs