That's correct to set the PF, but everytime you go back to Initial Print, you are starting over from scratch, so yes, everytime it goes back to its starting point, not the last calibration you did.
If you want to check it after a print then JUST do Confirm Print.
If it is changing at that point then you have an issue.
First thing to check is the encoder wheel for the pf motor - cleanliness and not touching the sensor.
Second, probably the sensor.
Load your media in the center of the machine, then place a piece of tape on the platen with part of it sticking under the media and part out.
Place a mark at the edge of the media.
You should be able to run out 5-6 feet without moving away from your mark significantly - say 1/16".
Media can wander depending on the slickness of the backer, so typically run with the media hold down in the most down position.