It cannot do that of course. When someone is new it often appears that the same action gets different results as they may have forgotten, or never knew the bits of information that the more experienced does not even think about but know out of hand.
If the design is not actually moved and the material is held firmly in place then the work will be done in the same place. If you have a good Calibration then Set Focus will align the image with where it will land. If you cannot do this then you need to run the Calibration again, If you align the image before Set Focus it will not be right. If you align without Set Focus the machine will Set Focus before running and it will be off also.
If everything is done right it will be right.