Could be the arc voltage value for the height sense is set too low.
Try sticking it up by 20 or 30 v it will be way too high but at least it will show you it is working.
if the height sense "picks up" after dragging for a short while - it could well be that the controller is not putting out a height sense disable signal.
after a pierce this should freeze the height sense until the machine has accellerated to about 90% of cutting speed. It should also freeze on corners.
depending on what sort of height sensor you have there is usually an indiction that the height sense disable is working.
from what i remember hypertherm units close a contact to disable the height sense. so if the cable breaks the hs is enabled al the time
hope this helps