is the position of the part being measured on the machine that made the part , by hand , or on a cmm ? What brand are your dials and bases , I've seen many cheaper brands creep (dial and base).
I may stand corrected but I believe the repeatability is supposed to be .0001"-.0002" , so this can be lost from the get go
True position can and will be affected by temps on a mill . A few minutes of a mill sitting idle is enough to throw off the positioning by up to a few tenths , I've experienced this on far better quality mills than a haas .
One way to ensure your not picking up slop is to always approach the part in the same angled direction on the x and y before starting the critical cuts . this will take up any slack if it exists .