Okay so for the last few days ive really been tuning in my J325 in and getting all the little bugs worked out, and one thing that was really bugging me was the way each axis moves when you reference it on start up, ive read so many different ways like flip each switch -.0500 before reference or to make a home program and send it there before shut off and so on, so I was bound and determined to figure out the right way so I setup dial indicators on each axis and started playing with it until I figured it out so I can use the home function send the machine home and shut it off and reference each axis to where it will reference the same every time without the axis moving at all.

So what you do is get your X Y Z axis where they are supposed to be arrow lined up on X and Y and the Z axis quill flush then re-reference your machine which puts the encoder on the master pulse for each axis then you have to use the machine zero function (not the zero set function) and this will set your machines home position right on the master pulse so when you send your machine home with the home function it will be right on the master pulse and bam you've got it!! Shut the machine off all you want and re-reference it without the axis moving as long as you send it home with the home function before shut down.

Hope this helps a few people