axis job image and toolpath image

Hi, I have a minor but annoying issue with my axis controller,, everything is working fine but when the job is running, the toolpath trace on the screen seems to be tracing roughly 1/4" (6mm) above the job image itself, no big deal but I would like to know why? is that normal or is there something I should alter?
cheers
Eric

Thanks, tommylight, I don't see any small green globes at the point where xyz are zeroed to the job, but some small circles at the home position, is that correct, I'm not sure I have a grasp on the coordinate system, reading up a bit now.
I did change the coordinates when I touched off from P0 (current) to P1 (G54) for each axis and the toolpath was right on the job image. more reading required I guess.
What I need is a dummies guide to it all, the documentation is getting harder for me to follow as I get older.