I have not personally seen what it does at the end of 1000 lines,
The goto z's button will make it go to a specified spot, default its somewhere like 3" above g53 z0(most home locations) Its in the settings page.
It would be a good idea to put a screw or something in the way of letting your machine travel off of its ways.
At first I was having troubles getting things to work right, eventually I figured everything out. If your doing tool changes, make sure to use your G43 H# offset(# is your tool number)
When I change a lot of settings, or even one, I always exit the program and make sure it saves, then it should be good even if something weird ends up happening afterwards.