Ok, thats possible - try making up some simple code to rapid (G0) the Z axis from Z0 to Z2 (or whatever travel you have, run it maybe 10 times starting from Z0 at a known position and at the end go to Z0 - is the axis in exactly the same position it was at the start???
If you are losing steps it could well be this, plus, when running THC you need to know that the normal acceleration curve is not used, THC moves on Z are more like BANG-BANG-BANG really fast moves are needed here or by the time the Z has moved the torch is elsewhere

I think there its a setting called THC-Rate - its a % of speed, try going low and working up, however i cant remember if this is a generic Mach3 setting or one specific to my screen set/THC system.
Test for lost steps first
EDIT
just saw TPS' reply - thats the box i mentioned.