Hey BLKKROW, I've had this happen to me before. Check the set screws on your x axis GT pulleys (the toothed belt gears). When the length of time the print is going increases, things start heating up and getting loose. I also seen the heat transfer from stepper motor to belt, heating them up slightly and making them loosen and skip a bunch of teeth causing the permanent shift.

Anyway, something to check! Tighten those belts and check the set screws.