I was about to report the same thing, for me its kinda game breaking as i use these values to prospect chunks say every 50 or 100 blocks and having the co-ordinates 'shifting' gives my OCD a bad time lol. Hopefully this issue is addressed before the next update.
Actually i read a bit more and just discovered that its normal for waypoint values to change once you change your spawn point, kinda a bummer this happens to be honest. Oh well ignore my particular comment for now, but would be good if changing your spawn point wouldn't shift all your waypoint values.
