Not sure, as i understand it, your z axis is not remembering where you set it before starting cutting i.e. you maybe set z zero with a gap of say 3mm between torch and work - it then cuts ok, moves up and down with THC but when finished, Z Zero is no longer 3mm form work??
Its hard to tell as my table has material height sense at the start of each cut so if it did lose position, it would reset it every time.
If you have a floating head, all you should need is a switch fitted in the right place, an input to the Probe input on Mach and some probing code, its pretty simple, oh and you need to alter your post processor IIRC to call the probe cycle before each pierce.