Ok, it sort of works

Had to move the soft limits 3mm as well but that made sense so ok.
Ref x/y worked good - it zeroed then set DRO's to -3mm as I wanted.
Cut a job - worked great,
Next job was in the middle of a part used sheet so I jogged to where I want, used "set ref point" to set my start location, cut job as normal.
Then I told it to ref x/y again and it only set to zero this time, no 3mm offset this time??
Restart mach and it works again.
So obviously I'm getting coordinates confused but is there a solution or can it not be done??