Sounds like it could be an interprative problem.
One tracks the orbit of electrons around an atom, while the other tracks the orbit of planets around a star.
One of these is less affected by tiny changes in spacetime by gravity. An atomic clock in space vs on earth will appear to desync eventually, but they are both 100% accurate if the machines correctly record orbit.
While an atomic clock will be perfectly correct, it doesn't track time at the same scale as our calenders attempt to. 

 Fab reply... learning. Thx