Safe Z is a user settable option, the M6 macro may well be telling it to go to the safe Z if you have it enabled. You can set the safe Z as machine coords or Work Coords or even an incremental position.
I still think the problem is you have a negative offset in the tooltable and you are using G43 rather than G44, It certainly seems to say that in the G Code list. Whether it is dependant on your safe Z setting I dont know.
Oh the safe Z setup is from the config menu.
Hood