OK you misunderstand what the Ref all is for. When you fist start the machine up you do the Ref All button and it will move each axis in turn to your home switches and it will let mach know where it is. This sets your machne coordinates up as X and Y zero at the lower left corner of your work area and for Z the zero is at its upermost. The important thing to remember this is machine coordinates and you dont often look at them. Now what you do is jog off to your material zero position but instead of pressing the Ref All button you press the zero for each axis, this will set up a work offset and it will show as zero in the DRO for each axis. However if you press the machine coords button you will see the DRO change to where Mach sees the true zero position to be (axis extremes).
This may not be causing your reversal problem but try it that way first and see.
Hood